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Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water.

A marine bacterial strain, designated FR1311T, was isolated from a sea-water sample from Ganghwa Island, South Korea. Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive, motile, oval or rod-shaped and halophilic (optimum sea-salt concentration for growth of 5-6 %). Phylogenetic analysis of its 16S rRNA gene sequence revealed that it represented a distinct line of descent within the genus Photobacterium. The major fatty acids were straight-chain saturated (C(16 : 0)) and monounsaturated fatty acids (C(16 : 1)omega7c and C(18 : 1)omega7c). The predominant respiratory lipoquinone was Q-8. The DNA G+C content was 44 mol%. The phenotypic features of strain FR1199T were similar to those of Photobacterium damselae subsp. damselae and Photobacterium damselae subsp. piscicida, but several physiological and chemotaxonomic properties readily distinguish the new isolate from them. On the basis of the polyphasic results revealed in this study, FR1311T is considered to be the type strain of a novel species, for which the name Photobacterium ganghwense sp. nov. is proposed. The type strain is FR1311T (=IMSNU 60287T = KCTC 12328T = JCM 12487T).

DNA, Bacterial↗

Study of genetic relationships among marine species of the genera Beneckea and Photobacterium by means of in vitro DNA/DNA hybridization.

Strains representative of species of the marine genera Beneckea and Photobacterium were used as reference standards in in vitro DNA/DNA competition experiments. Within a given species, strains were found to be related by over 80% competition. (Competition was defined as the amount of radioactive DNA displaced by heterologous DNA relative to the amount displaced by homologous DNA.) On the basis of interspecies competition values (expressed as averages), the following groupings could be made: 1. "Photobacterium" fischeri was related to strain ATCC 15382 by a competition of 38% and was distinct from all the other strains tested (competition less than or equal to 11%). 2. The genus Photobacterium consisted of 3 species, P.phosphoreum, P.leiognathi, and a newly designated species, P.angustum (composed of non-luminous strains). The latter species was found to be related to P.leiognathi and P.phosphoreum by 56 and 28% competition, respectively, while P.phosphoreum was related to P.leiognathi by 29%. 3. In the genus Beneckea, 65% competition was detected between B.harveyi and B.campbellii as well as between B.parahaemolytica and B.alginolytica. These pairs of species were related to each other by 51-58% and to B.natriegens by 34-56% competition. A newly designated pathogenic species, B.vulnifica, appeared to have a low but significant relationship to all the above mentioned species of Beneckea. 4. Two biotypes, related by 68% competition, were recognized in the species B.splendida. Similarly, B.pelagia was found to consist of 2 biotypes related by a competition of 67%. The competition values between these species were 38-40%. 5. B.nereida, B.nigrapulchrituda, and "Vibrio" anguillarum had competition values less than or equal to 30% to each other as well as to other species of Beneckea. 6. With Vibrio cholerae as the reference standard, V.albensis was found to be related by a competition of 82%, while V.proteus and V.metschnikovii had competition values of 22 and 12%, respectively. These results suggested that V.albensis should be synonymized with V.cholerae, while the latter two organisms should remain distinct from this species. V.cholerae as well as the other terrestrial organisms tested did not appear to be significantly related to any of the marine strains (competition values less than or equal to 27%). The speciation derived from the results of the DNA/DNA competition experiments was compared to previous speciation based on phenotypic similarities.

DNA, Bacterial↗

Physical characterization of lumazine proteins from Photobacterium.

The physicochemical properties of Photobacterium lumazine proteins have been investigated. The molecular weights obtained by several physical techniques are in good agreement, and the averages are 2% and 8% higher than the minimum molecular weights from amino acid and ligand content. The average molecular weights, sedimentation coefficients, and molecular radii are respectively the following: Photobacterium leiognathi lumazine protein, 21 200 +/- 300, 2.18 S, and 22.9 A; Photobacterium phosphoreum lumazine protein, 21 300 +/- 500, 2.16 S, and 23.0 A. The hydrations of the lumazine proteins, estimated in several ways, indicate less hydration for P. leiognathi than for P. phosphoreum. The frictional ratios corrected for hydration give axial ratios less than 1.3 for both lumazine proteins. These values agree with those obtained by a combination of rotational and translational frictional parameters and elimination of the common hydrated volume terms. There is insufficient area on the exterior surface to accommodate hydration when the lumzine proteins are considered as smooth-surfaced ellipsoids. The required surface area can be accommodated however by surface roughness with a minimum of 30% internal water.

Amino Acids↗

Formation of hybrid luciferases from subunits of different species of Photobacterium.

Enzyme divergence within three species of the genus Photobacterium (P. fischeri, P. leiognathi, and P. phosphoreum) was studied by comparing the catalytic characteristics and quaternary interactions of bacterial luciferases isolated from each species. Each luciferase was composed of two subunits of different molecular weights as determined by sodium dodecyl sulfate--polyacrylamide gel electrophoresis. Subunits were isolated in quantity by DEAE-Sephadex gel filtration in 7 M urea. Isolated subunits had no luciferase activity after renaturation in buffer, but active enzyme could be recovered by renaturation of the heavy and light subunits together. Renaturation of hybrid pairs (containing one subunit from each of two different species) yielded active luciferases, but only in cases where a heavy subunit of one species was combined with a light subunit of another. These hybrids exhibited in vitro catalytic characteristics most like those of the parent luciferase from which the heavy subunit was derived. The light subunit of P. leiognathi luciferase conferred an increased thermal stability to all enzymes containing it. The heavy subunit of each of the three Photobacterium species was sensitive to trypsinization. Thus, on the basis of structural and functional analogies with the luciferase from Beneckea harveyi, the heavy and light subunits of Photobacterium species have been designated alpha and beta, respectively.

Chromatography, Ion Exchange↗

Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences.

We sequenced nearly complete small-subunit rRNAs of 54 reference strains belonging to the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas. We then performed a phylogenetic analysis by comparing the sequences which we obtained with all other known sequences for bacteria belonging to the gamma subgroup of the Proteobacteria (thus providing a data base consisting of 70 sequences for the genera investigated), using methods such as neighbor joining, maximum likelihood, and maximum parsimony, as well as bootstrap, to assess the robustness of each topology. Our results confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species (but not Vibrio marinus); that Aeromonas species deserve family rank; and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae. The genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas, together with the family Enterobacteriaceae, the family Pasteurellaceae, and probably the genus Alteromonas, form a robust monophyletic unit within the gamma 3 subgroup of the Proteobacteria.

Aeromonas↗

Reassessment of the taxonomic position of Vibrio iliopiscarius (Onarheim et al. 1994) and proposal for Photobacterium iliopiscarium comb. nov.

The phylogenetic position of Vibrio iliopiscarius was inferred by the maximum-likelihood, maximum-parsimony and neighbour-joining methods on the basis of almost complete 16S rRNA gene sequences. The results showed that this species falls into the same cluster as Photobacterium species and is clearly distinct from other Vibrio species. Its nearest phylogenetic neighbour is Photobacterium phosphoreum. From these results, it is concluded that V. iliopiscarius should be reclassified as Photobacterium iliopiscarium comb. nov., the type strain of which is PS1T (= ATCC 51760T).

Base Sequence↗

The lux genes of the luminous bacterial symbiont, Photobacterium leiognathi, of the ponyfish. Nucleotide sequence, difference in gene organization, and high expression in mutant Escherichia coli.

The lux genes required for light expression in the luminescent bacterium Photobacterium leiognathi (ATCC 25521) have been cloned and expressed in Escherichia coli and their organization and nucleotide sequence determined. Transformation of a recombinant 9.5-kbp chromosomal DNA fragment of P. leiognathi into an E. coli mutant (43R) gave luminescent colonies that were as bright as those of the parental strain. Moreover, expression of the lux genes in the mutant E. coli was strong enough so that not only were high levels of luciferase detected in crude extracts, but the fatty-acid reductase activity responsible for synthesis of the aldehyde substrate for the luminescent reaction could readily be measured. Determination of the 7.3-kbp nucleotide sequence of P. leiognathi DNA, including the genes for luciferase (luxAB) and fatty-acid reductase (luxCDE) as well as a new lux gene (luxG) found recently in luminescent Vibrio species, showed that the order of the lux genes was luxCDABEG. Moreover, luxF, a gene homologous to luxB and located between luxB and luxE in Photobacterium but not Vibrio strains, was absent. In spite of this different lux gene organization, an intergenic stem-loop structure between luxB and luxE was discovered to be highly conserved in other Photobacterium species after luxF.

Aldehyde Oxidoreductases↗

Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.

Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

Animals↗

The primary structure of Cu-Zn superoxide dismutase from Photobacterium leiognathi: evidence for a separate evolution of Cu-Zn superoxide dismutase in bacteria.

The complete amino-acid sequence of the copper-zinc superoxide dismutase of the Photobacterium leiognathi was determined. The fragmentation strategy employed included cyanogen bromide cleavage at its methionine residues and the only tryptophan residue. The S-carboxymethylated chain was further cleaved by means of trypsin, in order to obtain overlapping fragments. For sequence determination automated solid or liquid-phase techniques of Edman degradation were used. C-Terminal amino acids of the entire chain were determined after treatment with carboxypeptidase A. Comparison of the primary structure of this bacterial Cu-Zn superoxide dismutase with the established amino-acid sequences of the other eukaryotic Cu-Zn superoxide dismutases revealed clear homologies. Correspondingly, the Cu-Zn-binding amino-acid residues of the active centre were localized: His45, His47, His70, His79, His125 and Asp91. The two cysteine residues in position 52 and 147 were homologous to the cysteine residues, modelling the essential intrachain disulfide bridge of the corresponding bovine enzyme. As only 25-30% of aligned sequence positions were found to be identical, the enzyme of P. leiognathi shows only a remote phylogenetic relationship towards eukaryotic Cu-Zn superoxide dismutases. When compared to the established phylogenetic tree of the cytochrome c family, this indicates a separate evolution of Cu-Zn superoxide dismutase in Photobacterium. Therefore, a natural gene transfer from the eukaryotic host (ponyfish) to the prokaryotic photobacterium, which Martin and Fridovich postulated 1981 (J. Biol. Chem. 256, 6080-6089) on the basis of amino-acid compositions, can be excluded.

Amino Acid Sequence↗

The complete nucleotide sequence of the lux regulon of Vibrio fischeri and the luxABN region of Photobacterium leiognathi and the mechanism of control of bacterial bioluminescence.

We have determined the complete nucleotide sequence of a 7622 base pair fragment of DNA from Vibrio fischeri strain ATCC7744 that contains all the information required to confer plasmid-borne, regulated bioluminescence upon strains of Escherichia coli. The lux regulon from V. fischeri consists of two divergently transcribed operons, L (left) and R (right), and at least seven genes, luxR (L operon) and luxICDABE (R operon) and the intervening control region. The luxA and luxB genes encode respectively the alpha and beta subunits of luciferase. The gene order luxCDABE seen in V. fischeri is the same as for V. harveyi. We have determined the sequence of the luxAB and flanking regions from Photobacterium leiognathi and have found upstream sequences homologous with luxC from the Vibrio species, but between luxB and luxE, there is an open reading frame encoding a protein of 227 amino acids (26,229 molecular weight) that is not found in this location in the Vibrio species. The amino terminal amino acid sequence of the encoded protein is nearly identical to that determined by O'Kane and Lee (University of Georgia) for the non-fluorescent flavoprotein from a closely related Photobacterium species (Dr Dennis O'Kane, personal communication). We have therefore designated this gene luxN. There is a 20-base inverted repeat ACCTGTAGGAxTCGTACAGGT, centred between bases 927 and 928 in the region between the two operons of V. fischeri. This region appears to fulfil two functions: it is critical for the LuxR protein to exert its effect and it is a consensus binding site for the E. coli LexA protein, a negative regulatory protein involved with the SOS response. There are sequences within the luxR coding region that appear to function in a cis-acting fashion to repress transcription from both the leftward and rightward promoters in the absence of the respective transcriptional activator proteins, thereby resulting in low basal levels of transcription. It now appears clear that there are multiple levels of control on the lux system allowing for a modulation of the intensity of bioluminescence of over four orders of magnitude.

Amino Acid Sequence↗

A Photobacterium-like bacterium able to fix nitrogen.

A Photobacterium-like bacterium isolated from the roots of eelgrass (Zostera marina) was shown to fix nitrogen under anaerobic conditions. Nitrogen fixation by Photobacterium spp. has not been reported previous to this.

Culture Media↗

Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi.

The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).

Animals↗

Heme uptake genes in human and fish isolates of Photobacterium damselae: existence of hutA pseudogenes.

The marine bacterium Photobacterium damselae includes strains classified into two distinct subspecies, namely subsp. damselae and subsp. piscicida, which have been reported to cause disease in a variety of marine animals and in humans. P. damselae strains utilize heme compounds as sole iron sources. In the present study, ten potential heme uptake and utilization genes are described in P. damselae subsp. damselae and subsp. piscicida. One gene cluster includes the genes coding for putative proteins HutZ, HutX and HutW; TonB, ExbB and ExbD, the three components of the TonB system; HutB, the putative periplasmic binding protein; HutC, the putative inner membrane permease; and HutD, the putative ABC-transporter ATP-ase. A gene coding for HutA, the outer membrane heme receptor, has also been identified, but it is not linked to the rest of the heme transport genes. RT-PCR analyses showed that heme uptake genes are arranged in three iron-regulated transcriptional units. A plasmid carrying the gene for the heme receptor HutA in combination with a plasmid carrying tonBexbBDhutBCD genes conferred to Escherichia coli 101ESD (ent) the ability to use heme and hemoglobin as iron sources. The hutA gene was present in strains isolated from humans and a variety of fish species, but it was shown to be interrupted in some subsp. piscicida strains, constituting a pseudogene. This is the first description of a heme-uptake system in a Photobacterium species, and shows some structural and functional similarities to heme-uptake systems reported in other gram-negative bacteria.

Amino Acid Sequence↗

New cold-adapted lipase from Photobacterium lipolyticum sp. nov. that is closely related to filamentous fungal lipases.

A Photobacterium strain, M37, showing lipolytic activity, was previously isolated from an intertidal flat of the Yellow Sea in Korea and identified as Photobacterium lipolyticum sp. nov. In the present study, the corresponding gene was cloned using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (1,023 bp) corresponded to a protein of 340 amino acid residues with a molecular weight of 38,026. No sequence similarity was found with any known bacterial lipases/esterases; instead, the most similar enzymes were several filamentous fungal lipases. Although the similarity was very low (less than 16%), there were many conserved regions over the entire sequence and N-terminal oxyanion hole (RG) region, a signature sequence of filamentous fungal lipases. The novel protein M37 was produced in both a soluble and insoluble form when the Escherichia coli cells harboring the gene were cultured at 18 degrees C. The soluble protein exhibited lipase activity in a pH-stat assay using an olive oil emulsion. The M37 lipase also displayed a maximum activity at 25 degrees C and maintained its activity at a low temperature range (5-25 degrees C) with an activation energy (E(a)) of 2.07 kcal/mol. Accordingly, these results indicate that the M37 lipase from P. lipolyticum sp. nov. is a new cold-adapted enzyme.

Amino Acid Sequence↗

Cloning and characterization of the gene encoding for OMP-PD porin: the major Photobacterium damsela outer membrane protein.

The outer membrane protein of Photobacterium damsela (OMP-PD) and the gene encoding for this porin protein were isolated and characterized. The deduced amino acid sequence of the OMP-PD monomer has 338 amino acids and a calculated molecular weight of 36,951 Da. This sequence includes a 22-amino acid signal peptide at the N-terminal, which is not found when the monomer is located in the outer membrane. Native OMP-PD protein forms a trimeric structure of approximately 110 kDa. It exhibits resistance to proteases, and it can be cleaved only following denaturation by SDS. The degree of identity of the OMP-PD amino acid sequence to porins from the Enterobacteriaceae was only 24%. Identity to Vibrio or Photobacterium porins was 38% and 48%, respectively. Nevertheless, the multiple alignment of this sequence with other structurally defined Enterobacteria porins demonstrated that the location of the 16 beta-strands and eight external loops, including a larger external L3 loop, are conserved in OMP-PD. These results, together with the previously known ability of OMP-PD to form an ion channel in artificial liposomes, strongly support its role as a porin in P. damsela and will help further investigations into the role of OMP-PD in P. damsela pathogenicity.

Amino Acid Sequence↗

The lux genes in Photobacterium leiognathi are closely linked with genes corresponding in sequence to riboflavin synthesis genes.

Three open reading frames (ORFs) have been found in the region downstream of the luxG gene in the Photobacterium leiognathi lux operon. These genes (ORF I, II, and III) are not only closely linked to the lux operon and transcribed in the same direction but also show the same organization and code for proteins homologous in sequence to the gene products of ribB, ribA, and ribH of Bacillus subtilis, respectively. The Photobacterium leiognathi gene (ORF II) corresponding to ribA was expressed in Escherichia coli in the bacteriophage T7 promoter-RNA polymerase system and a 40 kDa 35S-labeled polypeptide has been detected on SDS-PAGE. Expression of DNA extending from luxBEG to ORF II inserted between a strong promoter and a reporter gene and transferred by conjugation into Vibrio harveyi did not affect the expression of the reporter gene. The results provide evidence that neither promoter nor terminator sites were present in the DNA between the luxG and ORF II indicating that these genes might be part of the lux operon.

Amino Acid Sequence↗

The lumazine protein-encoding gene in Photobacterium leiognathi is linked to the lux operon.

The nucleotide (nt) sequence of the lumP (EMBL accession No. X65612) gene of Photobacterium leiognathi PL741 was determined and the amino acid (aa) sequence deduced. The encoded aa sequence of lumP was identified as that of the lumazine protein (LumP) by homology with that of Photobacterium phosphoreum (56%). This small protein has a calculated M(r) of 19,997 and comprises 186 aa residues. Biochemical studies suggested that LumP is the protein which, when combined with luciferase, is responsible for the bioluminescent spectrum shift from blue-green light (490-505 nm) to blue (470 nm) in P. leiognathi. The nt sequence of the flanking region showed that lumP is linked to the lux operon but runs in the opposite direction. The gene order of the lumP and lux operon is as follows: <--lumP-R&R-luxC-luxD-luxA-luxB-luxN-lu xE-->; the R&R regulatory region sequence included two promoter systems, PR for the lux operon and PL for the lumP or the lum operon.

Amino Acid Sequence↗

Spectral properties and function of two lumazine proteins from Photobacterium.

The spectral properties are compared for two 6,7-dimethyl-8-ribityllumazine proteins from marine bioluminescent bacteria, one from a psychrophile, Photobacterium phosphoreum, and the other from a thermophile, Photobacterium leiognathi. The visible spectral properties, which are the ones by which the protein performs its biological function of bioluminescence emission, are almost the same for the two proteins: at 2 degrees C and 50 mM Pi, pH 7, fluorescence quantum yield phi F = 0.59 and 0.54, respectively; fluorescence lifetime tau = 14.4 and 14.8 ns, respectively; fluorescence maxima, both 475 nm; absorption maximum, 417 and 420 nm, respectively; circular dichroism minima at around 420 nm, both -41 X 10(3) deg cm2 dmol-1. The ligand binding sites therefore must provide very similar environments, and arguments are presented that the bound ligand is relatively exposed to solvent. The dissociation equilibrium was studied by steady-state fluorescence polarization. The thermophilic protein binds the ligand with Kd (20 degrees C) = 0.016 microM, 10 times more tightly than the other protein [Kd (20 degrees C) = 0.16 microM]. The origin of the binding difference probably resides in differences in secondary structure. The tryptophan fluorescence spectra of the two proteins are different, but more significant is an observation of the decay of the tryptophan emission anisotropy. For the psychrophilic lumazine protein this anisotropy decays to zero in 1 ns, implying that its single tryptophan residue lies in a very "floppy" region of the protein. For the other protein, the anisotropy exhibits both a fast component and a slow one corresponding to rotation of the protein as a whole.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗