Biomedical subjects

Takashi Naka

Publications and source records attributed to Takashi Naka.

18 recordsLinked to original sources

PubMed2006

Structural characterization of a specific glycopeptidolipid containing a novel N-acyl-deoxy sugar from mycobacterium intracellulare serotype 7 and genetic analysis of its glycosylation pathway.

The nontuberculous Mycobacterium avium-Mycobacterium intracellulare complex (MAC) is distributed ubiquitously in the environment and is an important cause of respiratory and lymphatic disease in humans and animals. These species produce polar glycopeptidolipids (GPLs), and of particular interest is their serotype-specific antigenicity. Structurally, GPLs contain an N-acylated tetrapeptide-amino alcohol core that is glycosylated at the C terminal with 3,4-di-O-methyl rhamnose and at the d-allo-threonine with a 6-deoxy-talose. This serotype nonspecific GPL is found in all MAC species. The serotype-specific GPLs are further glycosylated with a variable haptenic oligosaccharide at 6-deoxy-talose. At present, 31 distinct serotype-specific GPLs have been identified on the basis of oligosaccharide composition, and the complete structures of 14 serotype-specific GPLs have been defined. It is considered that the modification of the GPL structure plays an important role in bacterial physiology, pathogenesis, and host immune responses. In this study, we defined the complete structure of a novel serotype 7 GPL that has a unique terminal amido sugar. The main molecular mass is 1,874, and attached to the tetrapeptide-amino alcohol core is the serotype 7-specific oligosaccharide unit of 4-2'-hydroxypropanoyl-amido-4,6-dideoxy-2-O-methyl-beta-hexose-(1-->3)-alpha-l-rhamnose-(1-->3)-alpha-l-rhamnose-(1-->3)-alpha-l-rhamnose-(1-->2)-alpha-l-6-deoxy-talose. Moreover, we isolated and characterized the serotype 7-specific gene cluster involved in glycosylation of the oligosaccharide. Nine open reading frames (ORFs) were observed in the cluster. Based on the sequence homology, the ORFs are thought to participate in the biosynthesis of the serotype 7 GPL.

Carbohydrate Sequence↗

PubMed2006

Mycobacterial sulfolipid shows a virulence by inhibiting cord factor induced granuloma formation and TNF-alpha release.

Virulence mechanism of infection with Mycobacterium tuberculosis is currently focused to be clarified in the context of cell surface lipid molecule. Comparing two mycobacterial glycolipids, we observed toxicity and prominent granulomatogenic activity of trehalose 6,6'-dimycolate (TDM) injection in mice, evident by delayed body weight gain and histological observations, whereas 2,3,6,6'-tetraacyl trehalose 2'-sulfate (SL) was non-toxic and non-granulomatogenic. Likewise, TDM but not SL caused temporarily, but marked increase of lung indices, indicative of massive granuloma formation. Interestingly, co-administration of TDM and SL prevented these symptoms distinctively and SL inhibited TDM-induced release of tumor necrosis factor alpha (TNF-alpha) in a dose-dependent manner. Histological findings and organ index changes also showed marked inhibition of TDM induced granuloma formation by co-administration of SL. Simultaneous injection of SL together with TDM was highly effective for this protection, as neither injection 1h before nor after TDM injection showed highly inhibitory. In parallel studies on a cellular level, TDM elicited strong TNF-alpha release from alveolar but not from peritoneal macrophages in vitro. This effect was blocked when alveolar macrophages were incubated in wells simultaneously coated with TDM and SL, indicating that SL suppresses TDM-induced TNF-alpha release from macrophages. Our results suggest a novel mechanism by which SL could contribute to virulence at early stage of mycobacterial infection or stimulation with the glycolipids by counteracting the immunopotentiating effect of TDM.

Animals↗

PubMed2006

Identification and characterization of the genes involved in glycosylation pathways of mycobacterial glycopeptidolipid biosynthesis.

Glycopeptidolipids (GPLs) are major components present on the outer layers of the cell walls of several nontuberculous mycobacteria. GPLs are antigenic molecules and have variant oligosaccharides in mycobacteria such as Mycobacterium avium. In this study, we identified four genes (gtf1, gtf2, gtf3, and gtf4) in the genome of Mycobacterium smegmatis. These genes were independently inactivated by homologous recombination in M. smegmatis, and the structures of GPLs from each gene disruptant were analyzed. Thin-layer chromatography, gas chromatography-mass spectrometry, and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analyses revealed that the mutants Deltagtf1 and Deltagtf2 accumulated the fatty acyl-tetrapeptide core having O-methyl-rhamnose and 6-deoxy-talose as sugar residues, respectively. The mutant Deltagtf4 possessed the same GPLs as the wild type, whereas the mutant Deltagtf3 lacked two minor GPLs, consisting of 3-O-methyl-rhamnose attached to O-methyl-rhamnose of the fatty acyl-tetrapeptide core. These results indicate that the gtf1 and gtf2 genes are responsible for the early glycosylation steps of GPL biosynthesis and the gtf3 gene is involved in transferring a rhamnose residue not to 6-deoxy-talose but to an O-methyl-rhamnose residue. Moreover, a complementation experiment showed that M. avium gtfA and gtfB, which are deduced glycosyltransferase genes of GPL biosynthesis, restore complete GPL production in the mutants Deltagtf1 and Deltagtf2, respectively. Our findings propose that both M. smegmatis and M. avium have the common glycosylation pathway in the early steps of GPL biosynthesis but differ at the later stages.

Bacterial Proteins↗

PubMed2005

Compensation effect of the MAPK cascade on formation of phospho-protein gradients.

The signal-transfer process in the mitogen-activated protein kinase (MAPK) cascade is formulated as a reaction-diffusion system describing the complete three-step phospho-protein reactions and the diffusion process in the direction from the cell membrane to the nucleus. The simulation analysis of the model demonstrates that MAPK cascade can work as a signal amplifier so as to compensate the signal attenuation due to formation of phospho-protein gradients. It also is found to be attainable for eukaryotic cells that a steep gradient of phosphorylated MAPK is not formed in a certain range of the system parameter values. One of the distinctive features in the formation of phospho-protein gradients is revealed to be its high sensitivity to a change in parameter values such as diffusion distance, diffusion coefficients and enzymatic activities of the phosphatases, suggesting that these parameters may act as the key factors for regulation of the signal transduction systems.

Animals↗

PubMed2005

Temperature-dependent biosynthesis of glucose monomycolate and its recognition by CD1-restricted T cells.

Mycolic acids are long chain fatty acids that constitute the lipid-rich cell wall framework of mycobacteria. Upon infection, mycobacteria begin to synthesize glucose monomycolate (GMM), a glucosylated species of mycolic acids, by utilizing host-derived glucose as sugar source. Accordingly, GMM production serves as a good indicator for local invasion of mycobacteria, and its detection by the host immune system would favor efficient monitoring of mycobacterial infection. Here, we found that GMM was produced abundantly at 30 degrees C rather than at 37 degrees C and recognized by a GMM-specific, CD1-restricted T cell line that was isolated from mycobacteria-infected human skin. Since the common portal sites for mycobacterial infection include ventilating alveoli of the lung and the externally exposed skin that often render invading microbes survive at reduced temperature, sampling GMM by CD1 lipid antigen-presenting molecules may allow the host to detect mycobacterial infection at its early phases.

Antigens, CD1↗

PubMed2005

Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry.

Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 microg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na]+ of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid (alpha, methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM from Mycobacterium tuberculosis showed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic) alpha-mycolates besides dicyclopropanoic mycolate, ranging from C75 to C85, odd- and even-carbon-numbered methoxymycolates ranging from C83 to C94 and even- and odd-carbon-numbered ketomycolates ranging from C83 to C90. In contrast, TMM from Mycobacterium bovis (wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoic alpha-mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in the Mycobacterium avium-intracellulare group, M. phlei and M. flavescens. The M. avium-intracellulare group possessed predominantly C85 and C87 wax ester-mycoloyl TMM, while M. phlei and the rapid growers tested contained C80, C81, C82 and C83 wax ester-mycoloyl TMM. This technique has marked advantages in the rapid analysis of not only intact glycolipid TMM, but also the mycolic acid composition of each mycobacterial species, since it does not require any degradation process.

Animals↗

PubMed2005

Intact molecular characterization of cord factor (trehalose 6,6'-dimycolate) from nine species of mycobacteria by MALDI-TOF mass spectrometry.

Cord factor (trehalose 6,6'-dimycolate, TDM) is an unique glycolipid with a trehalose and two molecules of mycolic acids in the mycobacterial cell envelope. Since TDM consists of two molecules of very long branched-chain 3-hydroxy fatty acids, the molecular mass ranges widely and in a complex manner. To characterize the molecular structure of TDM precisely and simply, an attempt was made to determine the mycolic acid subclasses of TDM and the molecular species composition of intact TDM by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for the first time. The results showed that less than 1 microg mycolic acid methyl ester of TDM from nine representative species of mycobacteria and TDM from the same species was sufficient to obtain well-resolved mass spectra composed of pseudomolecular ions [M+Na]+. Although the mass ion distribution was extremely diverse, the molecular species of each TDM was identified clearly by constructing a molecular ion matrix consisting of the combination of two molecules of mycolic acids. The results showed a marked difference in the molecular structure of TDM among mycobacterial species and subspecies. TDM from Mycobacterium tuberculosis (H37Rv and Aoyama B) showed a distinctive mass pattern and consisted of over 60 molecular ions with alpha-, methoxy- and ketomycolate. TDM from Mycobacterium bovis BCG Tokyo 172 similarly showed over 35 molecular ions, but that from M. bovis BCG Connaught showed simpler molecular ion clusters consisting of less than 35 molecular species due to a complete lack of methoxymycolate. Mass ions due to TDM from M. bovis BCG Connaught and Mycobacterium kansasii showed a biphasic distribution, but the two major peaks of TDM from M. kansasii were shifted up two or three carbon units higher compared with M. bovis BCG Connaught. Within the rapid grower group, in TDM consisting of alpha-, keto- and wax ester mycolate from Mycobacterium phlei and Mycobacterium flavescens, the mass ion distribution due to polar mycolates was shifted lower than that from the Mycobacterium avium-intracellulare group. Since the physico-chemical properties and antigenic structure of mycolic acid of TDM affect the host immune responses profoundly, the molecular characterization of TDM by MALDI-TOF mass analysis may give very useful information on the relationship of glycolipid structure to its biological activity.

Animals↗

PubMed2005

Use of glycopeptidolipid core antigen for serodiagnosis of mycobacterium avium complex pulmonary disease in immunocompetent patients.

We report the development of a serodiagnostic method for Mycobacterium avium complex (MAC) disease with an enzyme immunoassay (EIA) with the MAC-specific glycopeptidolipid (GPL) core as the antigen. In this study, we confirmed by EIA that the GPL core antibody was in the sera of immunocompetent patients with MAC disease. The EIA for quantifying the GPL core antibody was evaluated as a clinical tool for serodiagnosis of pulmonary MAC disease. A significant increase in GPL core antibodies (immunoglobulins G, A, and M) was detected in sera of patients with MAC pulmonary diseases when they were compared to patients who were colonized with MAC, patients with Mycobacterium kansasii disease or tuberculosis, and healthy subjects. The sensitivities and specificities of the GPL core-based EIA for diagnosis of MAC pulmonary disease were 72.6% and 92.2%, respectively, for IgG, 92.5% and 95.1%, respectively, for IgA, and 78.3% and 91.0%, respectively, for IgM. The best sensitivity and specificity were obtained by measuring immunoglobulin A antibodies against GPL core antigen. The level of GPL core antibodies reflected disease activity, since it decreased in cured MAC patients who had responded to chemotherapy. Measurement of serum antibodies against GPL core is useful for both diagnosis and assessment of disease activity in MAC disease of the lung.

Adult↗

PubMed2004

OBIYagns: a grid-based biochemical simulator with a parameter estimator.

UNLABELLED: OBIYagns (yet another gene network simulator) is a biochemical system simulator that comprises a multiple-user Web-based graphical interface, an ordinary differential equation solver and a parameter estimators distributed over an open bioinformatics grid (OBIGrid). This grid-based biochemical simulation system can achieve high performance and provide a secure simulation environment for estimating kinetic parameters in an acceptable time period. OBIYagns can be applied to larger system biology-oriented simulation projects. AVAILABILITY: OBIYagns example models, methods and user guide are available at https://access.obigrid.org/yagns/ SUPPLEMENTARY INFORMATION: Please refer to Bioinformatics online.

Algorithms↗

PubMed2004

Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir.

Four Gram-positive bacteria, strains A1-17B(T), A1-22(T), A1-3(T) and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17B(T)), Rhodococcus (A1-22(T)) and Arthrobacter (A1-3(T) and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17B(T) and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99.8, 98.0, 96.4 and 95.4 %. Polyphasic taxonomic evidence indicated that strain A1-17B(T) should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus ROTHIA: Strain A1-22(T) formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA-DNA relatedness values were only 45.5, 35.3, 18.9 and 21.9 %. Strains A1-3(T) and A1-8 shared 99.9 % 16S rDNA sequence similarity, and strain A1-3(T) showed the highest level of 16S rDNA similarity, 96.6 %, to Arthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17B(T)=GTC 867(T)=JCM 11412(T)=DSM 14556(T)), Rhodococcus baikonurensis sp. nov. (A1-22(T)=GTC 1041(T)=JCM 11411(T)=DSM 44587(T)) and Arthrobacter russicus sp. nov. (A1-3(T)=GTC 863(T)=JCM 11414(T)=DSM 14555(T)).

Air Microbiology↗

PubMed2004

Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir.

On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the genera Sphingomonas and Brevundimonas were identified from samples taken from the Russian space laboratory Mir. Strain A1-18(T) was isolated from the air. 16S rDNA sequence analysis showed that strain A1-18(T) formed a coherent cluster with Sphingomonas sanguinis, Sphingomonas parapaucimobilis, Sphingomonas paucimobilis and Sphingomonas roseiflava with sequence similarity of 97.5-98.6 %. Similar to other Sphingomonas species, the G+C content was 66.1 mol%, but DNA-DNA hybridization rates at optimal temperatures among these related species were only 24.7-51.7 %. Strain A1-18(T) can be differentiated biochemically from related species. Strain W1-2B(T) was isolated from condensation water. It forms a distinct lineage within the genus Brevundimonas, forming a coherent cluster with Brevundimonas vesicularis, Brevundimonas aurantiaca and Brevundimonas intermedia. 16S rDNA sequence similarities were 98.6-99.5 % and the G+C content was 66.5 mol%, similar to other Brevundimonas species, but DNA-DNA relatedness was only 50.2-54.8 %. Strain W1-2B(T) also showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species, Sphingomonas yabuuchiae sp. nov. (type strain A1-18(T)=GTC 868(T)=JCM 11416(T)=DSM 14562(T)) and Brevundimonas nasdae sp. nov. (type strain W1-2B(T)=GTC 1043(T)=JCM 11415(T)=DSM 14572(T)).

Air Microbiology↗

PubMed2003

Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium.

The unique feature of the genus Sphingobacterium is the presence of sphingophospholipids and ceramides, besides diacylglycerophospholipids. As major cellular lipid components, five kinds of sphingophospholipids were purified from Sphingobacterium spiritivorum ATCC 33861(T), the type species of genus Sphingobacterium. They were identified as ceramide phosphorylethanolamines (CerPE-1 and CerPE-2), ceramide phosphoryl-myo-inositols (CerPI-1 and CerPI-2), and ceramide phosphorylmannose (CerPM-1). The ceramide of CerPE-1, CerPI-1, and CerPM-1 was composed of 15-methylhexadecasphinganine (isoheptadeca sphinganine, iso-C17:0) and 13-methyltetradecanoic acid (isopentadecanoic acid, iso-C15:0), whereas that of CerPE-2 and CerPI-2 was composed of isoheptadeca sphinganine and 2-hydroxy-13-methyltetradecanoic acid (2-hydroxy isopentadecanoic acid, 2-OH iso-C15:0). These sphingophospholipids were also found in cellular lipids of Sphingobacterium multivorum ATCC 33613(T), Sphingobacterium mizutaii ATCC 33299(T), Sphingobacterium faecium IFO 15299(T), Sphingobacterium thalpophilum ATCC 43320(T), and Sphingobacterium antarcticum ATCC 51969(T). To our knowledge, the existence of CerPM-1 is a novel sphingophospholipid through eukaryotic and prokaryotic cells.

Ceramides↗

PubMed2003

A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling.

ErbB tyrosine kinase receptors mediate mitogenic signal cascade by binding a variety of ligands and recruiting the different cassettes of adaptor proteins. In the present study, we examined heregulin (HRG)-induced signal transduction of ErbB4 receptor and found that the phosphatidylinositol 3'-kinase (PI3K)-Akt pathway negatively regulated the extracellular signal-regulated kinase (ERK) cascade by phosphorylating Raf-1 on Ser(259). As the time-course kinetics of Akt and ERK activities seemed to be transient and complex, we constructed a mathematical simulation model for HRG-induced ErbB4 receptor signalling to explain the dynamics of the regulation mechanism in this signal transduction cascade. The model reflected well the experimental results observed in HRG-induced ErbB4 cells and in other modes of growth hormone-induced cell signalling that involve Raf-Akt cross-talk. The model suggested that HRG signalling is regulated by protein phosphatase 2A as well as Raf-Akt cross-talk, and protein phosphatase 2A modulates the kinase activity in both the PI3K-Akt and MAPK (mitogen-activated protein kinase) pathways.

Animals↗

PubMed2003

[Cu(H4C3N2S)Cl2](n), an unprecedented diazole-bridged one-dimensional copper halide: synthesis, structure, and magnetic properties.

The simultaneous desulfurization of 2-mercapto-5-methyl-1,3,4-thiadiazole with CuCl(2) x 2H(2)O via mutual diffusion in solvents results in the isolation of air-stable dark-green crystals of [Cu(H(4)C(3)N(2)S)Cl(2)](n) (approximately 65% yield). The structure is characterized by a unique one-dimensional copper chain bridged by diazine N-N single bonds rather than halogens, in sharp contrast with the halide bridging mode in conventional copper halide coordination polymers. Each Cu(II) ion shows a square planar coordination geometry featuring a strong Jahn-Teller distortion, as also supported by EPR data. The phase follows a Curie-Weiss paramagnetic behavior over 6-300 K. However, the intrachain antiferromagnetic interaction is evident (-2J = 21.1 cm(-1)). Such magnetic coupling is related to the interplay between the Cu(II)-d(x2-y2) and diazine N-N p-orbitals.

Journal Article↗

PubMed2003

Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir.

Classification of strain W3-B1, which was isolated from condensation water in the Russian space laboratory Mir, was investigated by a polyphasic taxonomic approach. Cells of strain W3-B1 were nonmotile, asporogenous, gram-negative slender rods with rounded ends. 16S rRNA gene sequence analysis indicated that organism should be placed in the genus Chryseobacterium. This organism contains menaquinone MK-6 as the predominent isoprenoid quinone and 3-OH iso 17:0 (40%), iso 15:0 (33%) as the major fatty acids. Phylogenetically, the nearest relative of strain W3-B1 is Chryseobacterium meningosepticum with sequence similarity of 98.4%, but DNA-DNA hybridization resulted in similarity values of only 52.3%. The G+C mol% is 34.6 mol%. Based upon results obtained by morphological, biochemical, chemotaxonomic, and molecular methods, strain W3-B1 was clearly distinguishable from other Chryseobacterium species. For these reasons, a novel species of family Flavobacteriaceae is proposed; strain W3-B1(T) (= GTC 862(T) = JCM 11413(T) = DSM 14571(T)) is the type strain.

Base Composition↗

PubMed2003

Bacterial ceramides and sphingophospholipids induce apoptosis of human leukaemic cells.

The genus Sphingobacterium, whose members are Gram-negative non-fermentative rods, possesses ceramides and related sphingophospholipids (SPLs) with isoheptadecasphinganine and 2-hydroxy or non-hydroxy isopentadecanoic acid. This paper reports evidence that ceramides isolated from Sphingobacterium spiritivorum ATCC 33861 induce endonucleolytic DNA cleavage in human myeloid leukaemia HL-60 cells in vitro, which is the primary characteristic biochemical marker for apoptosis or programmed cell death. Ceramides and SPLs also induced DNA fragmentation and caspase-3 activation, followed by changes in morphology, such as alterations in the size of nuclei and cells, and cell cycle shortening. Apoptotic activity correlated with the ceramide structure. Ceramide with a 2-hydroxy fatty acid showed stronger apoptotic activity than ceramide with a non-hydroxy fatty acid. Furthermore, the major five SPLs (ceramide phosphorylethanolamine-1 and -2, ceramide phosphorylinositol-1 and -2, and ceramide phosphorylmannose-1) showed apoptosis-inducing activity in HL-60 cells, indicating that the ceramide moiety of the SPLs plays a crucial role as the intracellular second messenger but that their hydrophilicity is less important in this regard. The hydrophilic part of SPLs may play a role in other cellular response systems. The involvement of Fas antigen was implicated in the apoptotic event since Fas antigen expression was observed after 3 or 4 h stimulation of HL-60 cells with bacterial ceramides. However, a time-course study for caspase-3 activation indicated maximal activity at 1 h after stimulation with bacterial ceramides, suggesting that two (or possibly more) mechanisms of signal transduction, Fas-dependent and Fas-independent, may be involved. Fas antigen expression and caspase-3 activation by five kinds of SPLs were observed after 3 or 4 h. These results indicate that there is a difference in the response of HL-60 cells to bacterial ceramides and SPLs.

Apoptosis↗

PubMed2002

Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola.

The 16S rDNA sequence similarities between the type strains of Sphingomonas paucimobilis and 32 other Sphingomonas species range from 90.2 to 99.6%. It might be possible to divide the genus into several new genera according to a dendrogram drawn from 16S rDNA sequence similarity. However, the phenotypic and biochemical information needed to define clusters of strains representing distinct genera within this group of organisms was not previously available. Although the cellular lipids of type strains of all 28 Sphingomonas species tested contained glucuronosyl-(1 --> 1)-ceramide together with 2-hydroxymyristic acid, other molecular species of sphingoglycolipids were distributed randomly. Sphingomonas natatoria and Sphingomonas ursincola, bacteriochlorophyll a-containing, gram-negative facultative phototrophs, belong to the cluster of the genus Sphingomonas. Other phototrophic Porphyrobacter and Erythrobacter species in the Sphingomonadaceae were classified into a cluster different from the genus Sphingomonas, as reported previously. None of the physiological and biochemical characteristics considered, including cellular lipids and fatty acid composition, provided evidence for the division of the current genus Sphingomonas. It is therefore concluded that the genus Sphingomonas should remain undivided at this time. The species of three recently proposed genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastobacter ursincola, are junior objective synonyms of species of the genus Sphingomonas.

Alphaproteobacteria↗

PubMed2002

Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits.

A polyphasic taxonomic study was performed on the phytopathogenic bacterial strains DAPP-PG 224(T) and DAPP-PG 228, which cause brown spot on yellow Spanish melon (Cucumis melo var. inodorus) fruits. Based on the presence of glucuronosyl ceramide (SGL-1) in cellular lipids, the results of fatty acid analysis and 16S rDNA sequence comparison, the strains had been identified as belonging to the genus Sphingomonas and as phylogenetically related to Sphingomonas mali, Sphingomonas pruni and Sphingomonas asaccharolytica. The levels of 16S rDNA sequence similarity of these three species to strain DAPP-PG 224(T) were respectively 98.0, 98.0 and 97.4%. DNA-DNA hybridization experiments between strains pathogenic on melon fruit and S. mali, S. pruni and S. asaccharolytica revealed < or = 16% relatedness. Based on these results, the two isolates studied are regarded as independent from the type strains of the three species mentioned above. Sphingomonas strains from melon fruits are recognized as forming a genetically and phenotypically discrete species and to be differentiated by phenotypic characteristics from all 29 named species of the genus. Thus, the name Sphingomonas melonis sp. nov. is proposed for the isolates from diseased melon fruits. The type strain is DAPP-PG 224(T) (= LMG 19484(T) = DSM 14444(T)). The G+C content of DNA of the type strain is 65.0 mol%.

Cucumis melo↗