• Korean Journal of Microbiology
• /
• v.30 no.1
• /
• pp.8-14
• /
• 1992

Nucleotide Sequence of phnE Gene Encoding Extradiol Dioxygenase fromPseudomonas sp. Strain DJ77Kim, Young-Chang'.", Myeong-Su Shin1, Kil-Sang Younl, Young-Soon Park1, andUg-Hyeon Kim'.' (Department of Microbiology, C'hungbuk National University.Cheongju 360-763, KOREA. and 'Research Center for Molecular Microbiology,Seoul National University)nal University)

• Korean Journal of Microbiology
• /
• v.33 no.1
• /
• pp.22-26
• /
• 1997

We cloned the 5~kb Xlwl fragment containing gene responsible for degrad"tion of phenanthrene using pBLUES~ CRIPT SK( +) vector and E. coli XLI-Blue strain from the genomic library of Pseudomonas sp. 0177 and this recombinant plasmid was named pUPX5. The strain containing pUPX5 could produce a yellow meta-cleavage product using 2.3-dihydroxybiphenyl as a substrate. This strain have a higher activity toward 2,3-dihydroxybiphenyl than catechol. We sub cloned and localized the gene encoding 2.3-dihydroxybiphenyl-1.2-dioxygenase. which is designated as phn$\Omega$.

• Korean Journal of Microbiology
• /
• v.30 no.1
• /
• pp.1-7
• /
• 1992

We cloned a gene cluster encoding phenanthrene-degrading enzymes on a 6.8-kb Xhol fragment from the Pseudomonas sp. DJ77 chromosomal DNA into the vector pBLUESCRIPT SIC(+). The resultant clone, containing the recombinant plilsmid pHENX7, was able to convert 3-methylcatechol to a yellow mela-cleavage compound. Since the pHENX7R in which the DNA insert was cloned in the opposite orientation lacked extradiol dioxygenase activity. the direction of transcription was established. Four polypeptides, PhnC (24 kDa). PhnD (31 kDa), PhnE (34 kDa). and PhnF (15 kDa), were identified in E coli JM101 transformed with several pHENX7-derived plasmids. The locations and extents of ~ndividual genes were determined by subcloning. The gene order was phnC-phnD-phnE-phnF-phnG, and phnC, phnD, phnE, and phnG genes encoded glutathione S-transferase, mrta-cleavage compound hydrolase, extradiol dioxygenase, mera-cleavage compound dehydrogenase, respectively.

• Journal of Microbiology and Biotechnology
• /
• v.9 no.3
• /
• pp.249-254
• /
• 1999

A catechol 2,3-dioxygenase (C23O) was purified to apparent homogeneity from Pseudomonas putida SU10 through several purification steps consisting of ammonium sulfate precipitation and chromatographies on DEAE 5PW, Superdex S-200, and Resource-Q. Gel filtration indicated a molecular mass under nondenaturing conditions of about 130 kDa. The enzyme has a subunit of 34 kDa as was determined by SDS-PAGE. These results suggest that the native enzyme is composed of four identical subunits. The N-terminal amino acid sequence (30 residues) of the enzyme has been determined and exhibits high identity with other extradiol dioxygenases. The reactivity of this enzyme towards catechol and methyl-substituted catechols is somewhat different from that seen for other catechol 2,3-dioxygenases, with 4-methylcatechol cleaved at a higher rate than catechol or 3-methylcatechol. $K_m$ values of the enzyme for these substrates are between 3.5 and 5.7 M.

• Journal of Microbiology and Biotechnology
• /
• v.12 no.1
• /
• pp.172-175
• /
• 2002

The complete nucleotide sequence of the nahC gene from Pseudomonas fluorescens, the structural gene for 1,2-dihydroxynaphthalene (1,2-DHN) dioxygenase, was determined. The 1,2-DHN dioxygenase is an extradiol ring-cleavage enzyme that cleaves the first ring of 1,2-dihydroxynaphthalene. The amino acid sequence of the dioxygenase deduced from the nucleotide sequence suggested that the holoenzyme consists of eight identical subunits with a molecular weight of approximately 34,200. The amino acid sequence of 1,2-DHN dioxygenase showed more than $90\%$ homology with those of the dioxygenases of other Pseudomonas strains. However, sequence similarity with those of the Sphingomonas species was less than $60\%$. The nahC gene of P. fluorescens was moderately expressed in E. coli NM522, as determined by enzymatic activity.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.5
• /
• pp.778-785
• /
• 2006

Catechol 1,2-dioxygenase was purified from cells of R. rhodochrous N75 grown at the expense of benzoate and p-toluate as the sole sources of carbon. A single catechol 1,2-dioxygenase was found to be induced with either growth substrate. The enzyme has an estimated $M_r$ of 71,000 consisting of two identical subunits. Catechol 1,2-dioxygenase from R. rhodochrous N75 exhibits some unusual properties including: broad substrate specificity, extradiol cleavage activity with 4-methylcatechol and low $K_m$ values for halocatechols, suggesting that this enzyme is distinct from other known catechol and chlorocatechol 1,2-dioxygenases.

• BMB Reports
• /
• v.32 no.4
• /
• pp.399-404
• /
• 1999

2,3-Dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD), which catalyzes the ring meta-cleavage of 2,3-dihydroxybiphenyl, is encoded by the phnQ gene of biphenyl- and phenanthrene-degrading Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1497 base pairs which included the phnQ gene. The fragment lncluded an open reading frame of 903 base pairs to accommodate the enzyme. The predicted amino acid sequence of the enzyme subunit consisted of 300 residues. In front of the gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli. The deduced amino acid sequence of the PhnQ enzyme exhibited 85.6% identity with that of the corresponding enzyme in Sphingomonas yanoikuyae Q1 (formerly S. paucimobilis Q1) and 22.1% identity with that of catechol 1,2,3-dioxygenase from the same DJ77 strain. PhnQ showed broader substrate preference than previously-cloned PhnE, catechol 2,3-dioxygenase. Ten amino acid residues, considered to be important for the role of extradiol dioxygenases, were conserved.

• Korean Journal of Microbiology
• /
• v.29 no.6
• /
• pp.392-396
• /
• 1991

Mu d1(Ap lac) bacteriophage can be used to search for genes which are members of a common regulatory network without having to know the functions of the genes in advance. Aim was for obtaining the loci in the SOS network as well as temperature inducible loci. For this purpose, recA441 allele was used. This allele encodes a thermosensitive recA gene product; thus, the recA441 allele can be activated upon temperature upshift without by external DNA damage. Approximately 10, 000 colonies were screened, and then searched for the colonies which expressed .betha.-galactosidase higher level at 42.deg.C than at 30.deg.C. The strains identified fell into two dlasses; (i) ones in which the increased expression was $recA^{+}$ $lexA^{+}$ -dependent, that is, din(damage-inducible) genes which were due to the activation of recA441 allele and (ii) ones in which the increased expression was $recA^{+}$ $lexA^{+}$ -independent and only temperature-inducible, tin genes. Rough mapping position was obtained for these genes.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2001.11a
• /
• pp.16-25
• /
• 2001

A genomic library of biphenyl-degrading strain Comamonas sp. SMN4 was constructed by using the cosmid vector pWE15 and introduced into Escherichia coli. Of 1,000 recombinant clones tested, two clones that expressed 2,3-dihydroxybiphenyl 1,2-dioxygenase activity were found (named pNB 1 and pNB2). From pNB1 clone, subclone pNA210, demonstrated 2,3-dihydroxybiphenyl 1,2-dioxygenase activity, is isolated. 2,3-Dihydroxybiphenyl 1,2-dioxygenase (23DBDO, BphC) is an extradiol-type dioxygenase that involved in third step of biphenyl degradation pathway. The nucleotide sequence of the Comamonas sp. SMN4 gene bphC, which encodes 23DBDO, was cloned into a plasmid pQE30. The His-tagged 23DBDO produced by a recombinant Escherichia coli, SG 13009 (pREP4)(pNPC), and purified with a Ni-nitrilotriacetic acid resin affinity column using the His-bind Qiagen system. The His-tagged 23DBDO construction was active. SDS-PAGE analysis of the purified active 23DBDO gave a single band of 32 kDa; this is in agreement with the size of the bphC coding region. The 23DBDO exhibited maximum activity at pH 9.0. The CD data for the pHs, showed that this enzyme had a typical a-helical folding structures at neutral pHs ranged from pH 4.5 to pH 9.0. This structure maintained up to pH 10.5. However, this high stable folding strucure was converted to unfolded structure in acidic region (pH 2.5) or in high pH (pH 12.0). The result of CD spectra observed with pH effects on 23DBDO activity, suggested that charge transition by pH change have affected change of conformational structure for 23DBDO catalytic reaction. The $K_m$ for 2,3-dihydroxybiphenyl, 3-metylcatechol, 4-methylcatechol and catechol was 11.7 $\mu$M, 24 $\mu$M, 50 mM and 625 $\mu$M.

• Journal of Microbiology and Biotechnology
• /
• v.8 no.3
• /
• pp.264-269
• /
• 1998

Commamonas acidovorans SMN4 showed wide growth substrate spectra for various aromatic hydrocarbons. Strain SMN4 was able to grow on biphenyl producing a meta-cleavage compound, yellow 2-hydroxy-6-oxophenylhexa-2,4-dienoic acid with a spray of 2,3-dihydroxybiphenyl, while it also grew on catechol, developing yellow 2- hydroxymucoic semialdehyde with a spray of 100 mM catechol. Thus these results indicate that two-ring structures of biphenyl were cleaved by meta-mode in upper and lower pathways. Strain SMN4 metabolized various substituted biphenyl compounds and xylene to the corresponding benzoate derivatives through oxidation of the ring structures. It was clearly shown that biphenyl can be a common inducer in the oxidation of biphenyl and 2,3-dihydroxybiphenyl. Various compounds were examined for their suitability to serve as substrates for indole oxidation, indicating that biphenyl, benzoate, and succinate are quite good inducers of indigo production due to the activity of biphenyl dioxygenase. This results suggest that indigo formation is by means of the combined activities of biphenyl dioxygenase and tryptophanase.