Versatile Transcription of Biphenyl Catabolic bphOperon in Pseudomonas pseudoalcaligenes KF707

Watanabe, Takeshi; Inoue, Ryo; Kimura, Nobutada; Furukawa, Koichi

doi:10.1074/jbc.m003023200

Cited by 49 publications

(66 citation statements)

References 34 publications

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“…The deduced gene product of ORF3A2-14, which was located upstream of dmpCDEFGH, is 43% identical to the Orf0 protein, a GntR-type transcriptional Aromatic catabolic pathways in microbial community H Suenaga et al regulator of the biphenyl-catabolizing (bph) operon of P. pseudoalcaligenes KF707 (Watanabe et al, 2000). Fosmid types 3A2 and 2C5 differ remarkably in that the two dmp gene clusters in 3A2 are separated by an intervening 10-kb sequence that does not appear to be involved in the degradation of aromatic compounds.…”

Section: Resultsmentioning

confidence: 99%

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

et al. 2009

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Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment.

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Section: Resultsmentioning

confidence: 99%

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

et al. 2009

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“…It is the case for TraR (44,76), 5 Found on the Web at sanger.ac.uk/Projects/Scoelicolor/. AphS and BphS (18,19), and FucR (51), which bind boxes with no clearly defined symmetrical properties. Thus, although the consensus sequences presented in Table II should be regarded as interesting tools, for instance, in making sequencing projects maximally useful, they certainly should not be considered as unerring references, and some GntR regulators should not fit with the general properties highlighted in this study.…”

Section: Resultsmentioning

confidence: 99%

Subdivision of the Helix-Turn-Helix GntR Family of Bacterial Regulators in the FadR, HutC, MocR, and YtrA Subfamilies

Rigali

Derouaux

Giannotta

et al. 2002

Journal of Biological Chemistry

328

475

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Among transcription factors, several groups have been identified according to their conserved motifs and their modes of DNA binding such as helix-turn-helix, zinc-fingers, leucinezipper, homeodomain, and ␤-sheet DNA-binding proteins (2, 3). The most studied and best characterized is the HTH 1 group (1, 4 -8) in which the conserved DNA recognition motif consists of an ␣-helix, a turn, and a second ␣-helix, often called the "recognition" helix as it is the part of the HTH motif that fits into the DNA major groove. Generally, HTH proteins bind as dimers, 2-fold symmetric DNA sequences in which each monomer recognizes a half-site. This group is now considered as a reference for understanding the general rules that govern protein-DNA interactions (9, 10) and has also become a favorite target for evolutionary studies (8,11).Among HTH transcriptional regulators, families have been identified throughout sequence comparisons and phylogenetic, structural, and functional analyses focused on DNA-binding domains and almost exclusively on the HTH structure, which is the only active motif that shows strong similarities among all members of the group (1, 4, 6 -8, 11). These comparative studies have led to the determination of a specific HTH consensus pattern or signature for each family, providing the basis for a simple method of classification and detection of new members (12).The lack of significant similarity among regions involved in effector binding or oligomerization systematically excludes these domains during families signature establishment, although they have important roles in the regulating process. In fact, it is often the oligomerization between regulatory subunits and/or the conformational changes due to the binding or the removal of the inducing/repressing molecule that allows correct HTH motif disposition and the subsequent DNA binding ability of the whole regulatory protein. The link between the two regions is therefore more intimate than it first appears from a unique amino acids comparison and may also be reflected in the DNA operator sequences, the third structural element involved in gene regulation.To argue for the existence of a link between regions involved in the regulating process, we analyzed the HTH GntR family of bacterial regulators. As determined thus far, the family comprises about 270 members distributed among the most diverse bacterial groups and regulating the most various biological processes. This family was first described by Haydon and Guest in 1991 (1) and was named after GntR, the repressor of the gluconate operon in Bacillus subtilis (13,14). Our interest in the properties of these bacterial regulators arises from the identification by our laboratory of the xlnR gene (15) in which chromosomal disruption in Streptomyces lividans relieves various extracellular enzymatic systems from glucose repression.The first purpose of this report is to present, 10 years after the first comparative study, an update of the GntR family description. Moreover, we decided to analyze the full-length sequenc...

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“…The translation product of orf0 is 58% similar to BphS, a GntR-like negative regulator of bph genes in Ralstonia eutropha A5 (37). Recently, other investigators found that in the PCB degrader Pseudomonas pseudoalcaligenes KF707 the translation product of orf0 is autoregulated and is necessary for expression of genes encoding enzymes in the biphenyl degradation pathway downstream of bphC (48). Induction of genes downstream of bphC allows cells to grow on biphenyl and minimizes the accumulation of metabolites resulting from biphenyl and PCB catabolism.…”

Section: Fig 2 Construction Of a Selectable Lacz Reporter Cassette mentioning

confidence: 99%

Induction of bphA , Encoding Biphenyl Dioxygenase, in Two Polychlorinated Biphenyl-Degrading Bacteria, Psychrotolerant Pseudomonas Strain Cam-1 and Mesophilic Burkholderia Strain LB400

Master

Mohn

2001

Appl Environ Microbiol

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We investigated induction of biphenyl dioxygenase in the psychrotolerant polychlorinated biphenyl (PCB) degrader Pseudomonas strain Cam-1 and in the mesophilic PCB degrader Burkholderia strain LB400. Using a counterselectable gene replacement vector, we inserted a lacZ-Gm r fusion cassette between chromosomal genes encoding the large subunit (bphA) and small subunit (bphE) of biphenyl dioxygenase in Cam-1 and LB400, generating Cam-10 and LB400-1, respectively. Potential inducers of bphA were added to cell suspensions of Cam-10 and LB400-1 incubated at 30°C, and then beta-galactosidase activity was measured. Biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately six times greater than the basal level in cells incubated with pyruvate. In contrast, the beta-galactosidase activities in LB400-1 incubated with biphenyl and in LB400-1 incubated with pyruvate were indistinguishable. At a concentration of 1 mM, most of the 40 potential inducers tested were inhibitory to induction by biphenyl of beta-galactosidase activity in Cam-10. The exceptions were naphthalene, salicylate, 2-chlorobiphenyl, and 4-chlorobiphenyl, which induced beta-galactosidase activity in Cam-10, although at levels that were no more than 30% of the levels induced by biphenyl. After incubation for 24 h at 7°C, biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately four times greater than the basal level in cells incubated with pyruvate. The constitutive level of beta-galactosidase activity in LB400-1 grown at 15°C was approximately five times less than the level in LB400-1 grown at 30°C. Thus, there are substantial differences in the effects of physical and chemical environmental conditions on genetic regulation of PCB degradation in different bacteria.

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Versatile Transcription of Biphenyl Catabolic bphOperon in Pseudomonas pseudoalcaligenes KF707

Cited by 49 publications

References 34 publications

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Subdivision of the Helix-Turn-Helix GntR Family of Bacterial Regulators in the FadR, HutC, MocR, and YtrA Subfamilies

Induction of bphA , Encoding Biphenyl Dioxygenase, in Two Polychlorinated Biphenyl-Degrading Bacteria, Psychrotolerant Pseudomonas Strain Cam-1 and Mesophilic Burkholderia Strain LB400

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