Identification of Xenobiotic-Degrading Isolates from the Beta Subclass of the Proteobacteria by a Polyphasic Approach Including 16S rRNA Partial Sequencing

Busse, Hans‐Jürgen; El-Banna, Tarek; Oyaizu, Hiroshi; Auling, Georg

doi:10.1099/00207713-42-1-19

Cited by 47 publications

(18 citation statements)

References 63 publications

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“…tardicrescens] LMG 9056 (the pathovar reference strain) contained hydroxyputrescine as a major polyamine and was identified as Acidovorax facilis (formerly Pseudomonasfacilis) by the TSBA data base (34). The presence of hydroxyputrescine is specific for organisms belonging to the beta subclass of the Proteobacteria (7,8). …”

Section: Methodsmentioning

confidence: 99%

Polyamine Patterns as Chemotaxonomic Markers for the Genus Xanthomonas

Yang

Vos

Kersters

et al. 1993

International Journal of Systematic Bacteriology

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Polyamine profiles of 140 Xbnthomonas strains were determined by high-performance liquid chromatography. The results revealed that there are two polyamine profiles within the genusXbnthmom. The first profile, characterized by spermidine as the major polyamine, was shared by Xbnthonwnas albilineans, Xiznthomoizas axonopodis, Xanthonwnas campestrk, Xbnthomonas fiagariae, Xbnthonwm oyzae, Xanthonwnas populi, and some unclassified xanthomonads. The second profile was typical of Xbnthonwlllls maftophiliu strains and contained spermidine and cadaverine as the major polyamines.According to the present taxonomy (5,20,23,24,32) PO-puli. All of these species except X. maltophilia are plant pathogens. The mounting evidence for the phylogenetic heterogeneity of X. campestris has been described previously (19, 25,28,30,31,34).In order to improve the taxonomy of the genus Xanthomonas (29), a polyphasic approach is now being used; this approach includes comparisons of sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) cellular protein profiles, DNA-DNA hybridization data, fatty acid analysis data, and polyamine patterns. The value of polyamine patterns for confirming phylogenetic relationships among phytopathogenic bacteria and other members of the Proteobacteria has been demonstrated previously (1,2,8). In addition, the difficulties in identification of gram-negative, aerobic, yellow-pigmented bacteria which are not associated with plants can be easily overcome by determining polyamine patterns (2). However, only six type strains and a few other Xanthomonas strains have been investigated previously, and spermidine was found to be the major polyamine in all strains. Three strains of X. maltophilia and one X. campestris strain (DSM 1350) had high cadaverine contents in addition to high spermidine contents, indicating the chemotaxonomic diversity of the genus Xanthomonas with regard to polyamine profiles (2). The reliability and potential use of polyamine contents as chemotaxonomic markers within the genus Xanthomonas suggested that a larger number of strains should be examined. In this paper we describe the results of a polyamine analysis of 148 strains, including 140 Xanthomonas strains; we examined members of all seven currently recognized species and some nonpathogenic Xanthomonas strains, and special emphasis was placed on X. maltophilia (57 X. maltophilia strains were examined). MATERIALS AND METHODSBacterial strains. The strains which we examined are listed in Table 1.Culture conditions. Bacterial strains from GYCA (1% [wt/vol] glucose, 0.5% [wt/vol] Extraction of polyamines. Polyamines were extracted by the procedure described by Scherer and Kneifel (21), with the following modifications: (i) the amount of the internal standard (1,B-diaminooctane) was 500 nmol, and the standard was dissolved in 0.2 M HC104 instead of water; and (ii) polyamines were extracted from fresh cells instead of freezedried cells.HPLC analysis of polyamines. The extracted dansylated polyamines were separated by using a high-per...

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Section: Methodsmentioning

confidence: 99%

Polyamine Patterns as Chemotaxonomic Markers for the Genus Xanthomonas

Yang

Vos

Kersters

et al. 1993

International Journal of Systematic Bacteriology

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“…The following strains of C. testosteroni were used: the type strain ATCC 11996, BR6020 (Providenti et al 2001), PSB-4 (DSM 11414) (Thurnheer et al 1986) and T-2 (DSM 6577) (Thurnheer et al 1986;Busse et al 1992). C. testosteroni was grown at 30°C in mineral salts medium (Thurnheer et al 1986;Junker et al 1996) containing a sole carbon source at 6 mM initial concentration on a 1.5-l scale, in 5-l shake flasks at 225 rpm.…”

Section: Methodsmentioning

confidence: 99%

Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases

2005

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Comamonas testosteroni T-2 degraded at least eight aromatic compounds via protocatechuate (PCA), whose extradiol ring cleavage to 2-hydroxy-4-carboxymuconate semialdehyde (HCMS) was catalysed by PCA 4,5-dioxygenase (PmdAB). This inducible, heteromultimeric enzyme was purified. It contained two subunits, a (PmdA) and b (PmdB), and the molecular masses of the denatured proteins were 18 kDa and 31 kDa, respectively. PCA was converted stoichiometrically to HCMS with an apparent K m of 55 lM and at a maximum velocity of 1.5 lkat. Structureactivity-relationship analysis by testing 16 related compounds as substrate for purified PmdAB revealed an absolute requirement for the vicinal diol and for the carboxylate group of PCA. Besides PCA, only 5¢-hydroxy-PCA (gallate) induced oxygen uptake. The Nterminal amino acid sequence of each subunit was identical to the corresponding sequences in C. testosteroni BR6020, which facilitated sequencing of the pmdAB genes in strain T-2. Small differences in the amino acid sequence had significant effects on enzyme stability. Several homologues of pmdAB were found in sequence databases. Residues involved in substrate binding are highly conserved among the homologues. Their sequences grouped within the class III extradiol dioxygenases. Based on our biochemical and genetic analyses, we propose a new branch of the heteromultimeric enzymes within that class.

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“…Positions 1 through 31 and 1376 through 1542 (E. coZi nomenclature [42]) were omitted from the analysis. In order to include restricted information for about 150 nucleotides of the 16s rRNAs from additional members of the beta subclass of the Proteubacteria (6,9), all of the sequences of the reference organisms were shortened to the same length in an additional comparison. Equally weighted (Hamming distances) and percent similarities between each pair of sequences were calculated.…”

Section: Methodsmentioning

confidence: 99%

“…As pointed out by Willems et al (36), all of the other Pseudomonas species are considered to be misclassified. Chemotaxonomy provides a rapid alternative approach for excluding organisms from or including organisms in the authentic pseudomonad taxon on the basis of the results of fatty acid, ubiquinone, and polyamine analyses (1, 2, [8][9][10]27). Below, those organisms that have the genus name Pseudomonas, but are not part of the phylogenetic nucleus of the true pseudomonad taxon (see above) are indicated by enclosing the genus name in single quotation marks (e.g., 'Pseudomonas' cepacia).…”

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confidence: 99%