Sequence Analysis of thephnDGene Encoding 2-Hydroxymuconic Semialdehyde Hydrolase inPseudomonassp. Strain DJ77

Shin, Hee-Jung; Kim, Seong-Jae; Kim, Young-Chang

doi:10.1006/bbrc.1997.6279

Cited by 23 publications

(12 citation statements)

References 22 publications

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“…strain HV3, 76) Sphingomonas sp. strain DJ77, [77][78][79] S. paucimobilis strain TNE12, 80) Sphingobium sp. strain P2 (Pinyakong, O., Habe, H., Yoshida, T., Nojiri, H., Omori, T., in preparation).…”

Section: (Vi) Pah-catabolic Genes Of Sphingomonas and Its Related Spementioning

confidence: 99%

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

Habe

Omori

2003

Bioscience, Biotechnology, and Biochemistry

382

220

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Section: (Vi) Pah-catabolic Genes Of Sphingomonas and Its Related Spementioning

confidence: 99%

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

Habe

Omori

2003

Bioscience, Biotechnology, and Biochemistry

382

220

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“…A bphK requirement could well depend on specific features of bphK genes in biphenyl degraders bphD) and an extradiol dioxygenase (e.g. phnE, an analogue of bphC) that are possibly involved in PAH catabolism (Lloyd-Jones & Lau, 1997 ;Shin et al, 1997). Upstream adjacent genes have thus far only been desribed for bphK of strain F199.…”

Section: Analysis Of Strain Lb400 and Other Bp M Bacteria For The Occmentioning

confidence: 99%

Occurrence and expression of glutathione-S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria

et al. 1999

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The gene bphK of Burkholderia sp. strain LB400 has previously been shown to be located within the bph locus, which specifies the degradation of biphenyl (BP) and chlorobiphenyls, and to encode a glutathione S-transferase (GST) which accepts 1-chloro-2,4-dinitrobenzene (CDNB) as substrate. The specific physiological role of this gene is not known. It is now shown that the gene is expressed in the parental organism and that GST activity is induced more than 20-fold by growth of the strain on BP relative to succinate when these compounds serve as sole carbon source. Approximately the same induction factor was observed for 2,3-dihydroxybiphenyl 1,2-dioxygenase activity, which is encoded by the 5'-adjacent bphC gene. This suggests that the expression of bphK is coregulated with the expression of genes responsible for the catabolism of BP. A bphK probe detected only a single copy of the gene in strain LB400. A spontaneous BP N mutant of the organism neither gave a signal with the bphK probe nor showed CDNB-accepting GST activity, suggesting that this activity is solely encoded by bphK. Complementation of the mutant with a bph gene cluster devoid of bphK restored the ability to grow on BP, indicating that bphK is not essential for utilization of this carbon source. BphK activity proved to be almost unaffected by up to 100-fold differences in proton concentration or ionic strength. The enzyme showed a narrow range with respect to a variety of widely used electrophilic GST substrates, accepting only CDNB. A number of established laboratory strains as well as novel isolates able to grow on BP as sole carbon and energy source were examined for BphK activity and the presence of a bphK analogue. CDNB assays, probe hybridizations and PCR showed that several, but not all, BP degraders possess this type of GST activity and/or a closely related gene. In all bacteria showing BphK activity, this was induced by growth on BP as sole carbon source, although activity levels differed by up to 10-fold after growth on BP and by up to 60-fold after growth on succinate. This resulted in a variation of induction factors between 2 and 30. In the majority of bphK M bacteria examined, the gene appeared to be part of LB400-like bph gene clusters. DNA sequencing revealed almost complete identity of bphK genes from five different bph gene clusters. These results suggest that bphK genes, although not essential, fulfil a strain-specific function related to the utilization of BPs by their host organisms. The usefulness of BphK as a reporter enzyme for monitoring the expression of catabolic pathways is discussed.

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“…Recently, Kim (1999) discovered that the organism was capable of metabolizing a variety of monocyclic aromatic hydrocarbons such as toluene, m-xylene, phenol, salicylate, benzoate and p-cresol, in addition to polycyclic aromatic compounds. Due to its ability to degrade a broad range of aromatic hydrocarbons, additional studies of metabolic pathways, enzymology and molecular mechanisms have been carried out for this strain (Jung et al, 1996 ;Kim et al, 1997a, b ;Shin et al, 1997 ;Hwang et al, 1999 ;Kim et al, 1999). A comparative study showed that the genes and gene orders for aromatic hydrocarbon degradation of strain DJ77 T were strikingly similar to the corresponding genes of Sphingomonas species, such as Sphingomonas paucimobilis EPA505, Sphingomonas yanoikuyae B1, ' Sphingomonas agrestis ' HV3 and Sphingomonas aromaticivorans F199 (Mueller et al, 1990 ;Kim, 1996 ;Yrja$ la$ et al, 1997 ;Romine et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

“…on the basis of the limited number of morphological and physiologic properties (Kim et al, 1986). Recently, Kim (1999) this strain (Jung et al, 1996 ; Kim et al, 1997a, b ;Shin et al, 1997 ;Hwang et al, 1999 ;Kim et al, 1999). A comparative study showed that the genes and gene orders for aromatic hydrocarbon degradation of strain DJ77 T were strikingly similar to the corresponding genes of Sphingomonas species, such as Sphingomonas paucimobilis EPA505, Sphingomonas yanoikuyae B1, ' Sphingomonas agrestis ' HV3 and Sphingomonas aromaticivorans F199 (Mueller et al, 1990 ;Kim, 1996 ;Yrja$ la$ et al, 1997 ;Romine et al, 1999).…”

mentioning

confidence: 99%

Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.

Kim¹,

Chun²,

Bae³

et al. 2000

International Journal of Systematic and Evolutionary Microbiology

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Pseudomonas sp. strain DJ77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. Phylogenetic analysis based on 16S rDNA sequences indicated that the strain belonged to the genus Sphingomonas and formed a monophyletic clade with the type strains of Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae with sequence similarity values of 981, 961 and 956 %, respectively. Genomic relatedness based on DNA-DNA hybridization of strain DJ77 to these strains is 7-14 %. Strain DJ77 contained ubiquinone 10 as the main respiratory quinone, and the GMC content of DNA was 63 mol %. The organism contained octadecenoic acid (67 %) as major cellular fatty acid. Strain DJ77 can be readily differentiated from representative members of the genus Sphingomonas using a battery of biochemical tests. On the basis of polyphasic evidence, it is proposed that strain DJ77, previously known as Pseudomonas sp., be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. The type strain is strain DJ77 T (l KCTC 2955 T l IMSNU 11152 T ).Keywords : Sphingomonas chungbukensis sp. nov., polyphasic classification, 16S rDNA sequencing, DNA-DNA hybridization INTRODUCTIONStrain DJ77 T , which degrades biphenyl and phenanthrenes, was isolated from contaminated sediment of an industrial complex near Taejon, Republic of Korea, and subsequently identified as Pseudomonas sp. on the basis of the limited number of morphological and physiologic properties (Kim et al., 1986). Recently, Kim (1999) this strain (Jung et al., 1996 ; Kim et al., 1997a, b ;Shin et al., 1997 ;Hwang et al., 1999 ;Kim et al., 1999). A comparative study showed that the genes and gene orders for aromatic hydrocarbon degradation of strain DJ77 T were strikingly similar to the corresponding genes of Sphingomonas species, such as Sphingomonas paucimobilis EPA505, Sphingomonas yanoikuyae B1, ' Sphingomonas agrestis ' HV3 and Sphingomonas aromaticivorans F199 (Mueller et al., 1990 ;Kim, 1996 ;Yrja$ la$ et al., 1997 ;Romine et al., 1999). The members of the genus Sphingomonas have been reported to degrade various aromatic hydrocarbons (Wittich et al., 1992 ;Ka et al., 1994 ; Fredrickson et al., 1995 ;Khan et al., 1996). In this study, we applied a polyphasic approach to identify strain DJ77 T . On the basis of chemotaxonomic, physiological and molecular systematic evidence, we propose that Pseudomonas sp. strain DJ77 T be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. Sphingomonas chungbukensis sp. nov. METHODSBacterial strains and cultures. Strain DJ77 T , S. chlorophenolica DSM 7098 T , S. herbicidovorans DSM 11019 T and S. yanoikuyae KCTC 2818 T were grown on Trypticase soy agar (TSA ; BBL) at 28 mC. Morphology. The morphological properties were examined after growth on TSA at 28 mC for 2 d by light microscopy and scanning electron microscopy (JEOL model JSM-6400). Determination of physiological characteristics. The oxidation of 95 different ca...

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Sequence Analysis of thephnDGene Encoding 2-Hydroxymuconic Semialdehyde Hydrolase inPseudomonassp. Strain DJ77

Cited by 23 publications

References 22 publications

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

Occurrence and expression of glutathione-S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria

Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.

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