Koei Hamana

Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus Sphingomonas can be divided into four clusters. Some chemotaxonomic and phenotypic differences were noted among these clusters. Three new genera, Sphingobium, Novosphingobium and Sphingopyxis, are proposed in addition to the genus Sphingomonas sensu stricto. The genus Sphingobium is proposed to accommodate Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae. The genus Novosphingobium is proposed for Sphingomonas aromaticivorans, Sphingomonas capsulata, Sphingomonas rosa, Sphingomonas stygia, Sphingomonas subarctica and Sphingomonas subterranea. Sphingomonas macrogoltabidus and Sphingomonas terrae are reclassified in the genus Sphingopyxis. The type species of Sphingobium, Novosphingobium and Sphingopyxis are Sphingobium yanoikuyae, Novosphingobium capsulatum and Sphingopyxis macrogoltabida, respectively.

Polyamines as a chemotaxonomic marker in bacterial systematics.

Aliphatic linear polyamines, from diamines to hexaamines, tertiary branched tetraamines, and quaternary branched pentaamines are widely distributed in eubacteria, archaebacteria, and cyanobacteria. Twenty-four linear types and four branched types are acid extractable from bacterial cells and can be chromatographically analyzed and identified. The varieties of polyamines are due to the combination of amino acid decarboxylase activities to form diamines, aminopropyl- and aminobutyl-transfer activities mediated by aminopropyltransferases or Schiff-base complex formation, and hydroxylation activity. The absence or presence of spermidine, norspermidine or homospermidine and the occurrence of 2-hydroxyputrescine and diaminopropane are related to grouping into the alpha, beta, gamma, and delta subclasses within Proteobacteria. Flavobacterium complex and green bacteria contain putrescine and homospermidine. Gram-negative thermophiles contain long linear and branched polyamines; however, their distribution profiles are species specific. Gram-positive eubacteria, which comprise Bacillus cluster, anaerobes, and actinomycetes, ubiquitously contain putrescine and spermidine, while the occurrence of spermine is limited to thermophiles. Archaebacteria are separated into polyamine-absent methanogens and halophiles, homospermidine-dominant methanogens, spermidine-dominant methanogens, and spermidine- and norspermidine-containing thermophiles. Cyanobacteria comprise two types; one group contains homospermidine and the other spermidine. The polyamine distribution pattern can serve as a chemotaxonomic marker in bacterial classification and is associated with bacterial systematics on the level of order, family, or genus.

Taxonomic Study of Bacteria Isolated from Plants: Proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.

The taxonomic positions of 10 strains of 3-ketolactose-forming bacteria which were isolated from the roots of plants (Rosa sp., Psychotria nairobiensis, Ardisia crispa, Prunus persica, and apple trees) were investigated. The DNA base compositions of these strains ranged from 64.0 to 65.7 mol%, the isoprenoid quinone of each strain was ubiquinone 10, 3-hydroxy fatty acids were lacking in the cellular fatty acids of these organisms, and all of the strains contained a sphingolipid with the long-chain base dihydrosphingosin. These are characteristics of the genus Sphingomonas. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S ribosomal DNA sequence comparison data, we propose the following four new species of the genus Sphingomonas: Sphingomonas rosa (type strain, IFO 15208) for the strains isolated from rose plants and formerly named [Agrobacterium rhizogenes]; Sphingomonas pruni (type strain, IFO 15498) for the strains isolated from Prunus persica; and Sphingomonas asaccharolytica (type strain, IFO 15499) and Sphingomonas mali (type strain, IFO 15500) for the strains isolated from apple trees. Two strains which were isolated from Psychotria nairobiensis and formerly named [Chromobacterium lividum] were identified as Sphingomonas yanoikuyae strains.

Occurrence in high concentrations of N1-acetylspermidine and sym-homospermidine in the hamster epididymis

Abstract In mature hamster epididymis several unknown peaks were observed on our high-performance liquid chromatograms in addition to the common polyamines, putrescine, spermidine and spermine. Three of the peaks were identified as N1-acetylspermidine, N1-acetylspermine and sym-homospermidine by means of thin-layer chromatography, gas chromatography-mass spectrometry and acid hydrolysis. The concentrations of N1-acetylspermidine and sym-homospermidine were highest in the distal caput epididymidis among epididymal regions studied. This is the first report to show that sym-homospermidine occurs in mammalian tissues.

Systematic analysis of naturally occurring linear and branched polyamines by gas chromatography and gas chromatography—mass spectrometry

Abstract Using heptafluorobutyryl derivatives of a series of 27 linear di-, tri-, tetra-, penta- and hexaamines containing various sets of isomers, and a series of four tertiary tetraamines and five quaternary pentaamines, mostly with three or four methylene chain units, their gas chromatographic (GC) and gas chromatographic—mass spectrometric (GC—MS) properties were compared and examined in detail. Several results useful for their systematic analysis were found: assured baseline separation of one methylene difference in linear di- and polyamines and tertiary tetraamines by GC; distinct pyrolytic decomposition patterns of quaternary pentaamines by GC; distinct cleavage patterns of three or four methylene chain units by GC—MS; and distinct mass spectra of linear polyamines and tertiary tetraamines by GC—MS.

Occurrence of sym-homospermidine as the major polyamine in nitrogen-fixing cyanobacteria

We analyzed the amount of polyamines in a variety of cyanobacteria including nitrogen-fixing and nonfixing species. All the cyanobacteria capable of fixing nitrogen, contained sym-homospermidine as the major polyamine. The concentration of putrescine, spermidine and spermine was extremely low in these cyanobacteria. The cyanobacteria which normally fail to fix nitrogen contained spermidine as the major polyamine, while the sym-homospermidine content was very low or under the limits of detection. Apparently there is a close relationship between the sym-homospermidine content and the ability to fix nitrogen in cyanobacteria.

Alterations in polyamine levels of nematode, earthworm, leech and planarian during regeneration, temperature and osmotic stresses

Free-living nematodes, Caenorhabditis elegans and Dorylaimus fodori, contain putrescine and spermidine. Putrescine, spermidine and spermine occur in the parasitic Nematoda, Ascaris suum, Anisakis simplex and Dirofilaria immitis. Earthworms, Eisenia foetida, Tubifex hattai and Pheretima communissima and the leech, Hirudo nipponia (belonging to Annelida) and the planarian, Dugesia japonica (belonging to Platyhelminthes) contain homospermidine and spermine in addition to putrescine and spermidine. Regenerated heads of E. foetida and D. japonica are rich in putrescine indicating the stimulation of its synthesis during regeneration. Putrescine and spermidine levels temporarily increase after heat shock in C. elegans, E. foetida and D. japonica and cold shock and hypertonic osmotic shock treatments in D. japonica.

Reclassification of Cytophaga aprica (Lewin 1969) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga diffluens (ex Stanier 1940; emend. Lewin 1969) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter diffluens comb. nov.

Phylogenetically, Cytophaga aprica and Cytophaga diffluens occupy independent positions in the flavobacter-bacteroides phylum. Both of these organisms are gram-negative rods that are motile by gliding, chemoorganotrophic, and aerobic, degrade several kinds of biomacromolecules, and inhabit marine environments. Their major isoprenoid quinone is menaquinone 7. The G+C content of the DNA of C. aprica is 35 to 37 mol%, and the G+C content of the DNA of C. diffluens is 40 to 42 mol%. In addition to constituting an independent phylogenetic lineage, each species has a distinctive cellular polyamine constitution. C. aprica is characterized by possessing cadaverine as its major polyamine, and C. diffluens is characterized by possessing spermidine, in contrast to most species of the genera Cytophaga, Flavobacterium, and Flexibacter and related organisms, which possess homospermidine. Transfer of C. aprica to the genus Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and transfer of C. diffluens to the genus Persicobacter gen. nov. as Persicobacter diffluens comb. nov. are proposed.

Occurrence of sym-homosphermidine in the Japanese newt, Cynops pyrrhogaster pyrrhogaster

During the course of study on polyamines in lower vertebrates, we encountered the presence of a prominent ninhydrin-positive peak which eluted posterior to spermidine on our amino acid analyzer. The concentration of this peak was particularly high in tissues of the Japanese red-bellied newt, @naps pyrrhogaster pyrrhogaster. Using both amino acid analysis and two-dimensional paper chromatography, we tested the unknown peak in various tissues of the newt. Our results demonstrate that the peak is composed of sym-homospermidine (1 Qdiaminodazanonane). The presence of this polyamine has not been reported in the animal world, though it was detected in leaves of sandalwood tree [l] and in some algae [2,3]. This paper describes the identification and measurement of sym-homospermidine in the newt.

Linear and branched pentaamines, hexaamines and heptaamines in seeds of Vicia sativa

Abstract We found new pentaamines, hexaamines and heptaamines which are aminobutyl derivative of homospermine (PA 444), in addition to four tetraamines, spermine (PA 343), thermospermine (PA 334), aminopropylhomospermidine (PA 344) and homospermine, in extracts of the mature seeds of the vetch Vicia sativa by HPLC and GC. Two linear polyamines were identified as homopentamine [NH 2 (CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ] (PA 4444) and homohexamine [NH 2 (CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ] (PA 44444) by GC-mass analysis. Another eight tertiary branched polyamines were identified as N 5 -aminobutylhomospermine [NH 2 (CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ][PA 4(4)44], N 5 -aminobutylhomopentamine [NH 2 (CH 2 ) 4 N-(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ](PA 4(4)444), N 10 -aminobutylhomopentamine[NH 2 (CH 2 ) 4 -NH(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ] [PA 44(4)44], N 5 , N 10 -bis(aminobutyl)homospermine [NH 2 (CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH 2 ] [PA 4(4)4(4)4)], N 5 -aminobutylhomohexamine [NH 2 -(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ] [PA 4(4)4444], N 10 -aminobutylhomohexamine [NH 2 (CH 2 ) 4 NH(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH(CH 2 ) 4 NH2] [PA44(4)444], N 5 , N 10 -bis(aminobutyl)-homopentamine [NH 2 (CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 NH(CH 2 ) 4 NH 2 ] [PA 4(4)4(4)44] and N 5 , N 15 -bis(aminobutyl)homopentamine [NH 2 (CH 2 ) 4 N(NH 2 (CH 2 ) 4 ) (CH 2 ) 4 NH(CH 2 ) 4 N(NH 2 (CH 2 ) 4 )(CH 2 ) 4 )NH 2 ] [PA 4(4)44(4)4].