A Tryptophan Pyrrole-Ring Cleavage Enzyme in the Most Primitive Eukaryote

1996 ◽  
pp. 441-447 ◽  
Author(s):  
Y. Iwamoto ◽  
I. S. Matsui Lee ◽  
M. Tsubaki ◽  
R. Kido
Keyword(s):  
Pyrrole Ring ◽  
Ring Cleavage ◽  
Cleavage Enzyme

Differential Roles of Three Different Upper Pathway Meta Ring Cleavage Product Hydrolases in the Degradation of Dibenzo- p -dioxin and Dibenzofuran by Sphingomonas wittichii RW1

2021 ◽  
Author(s):  
Thamer Y. Mutter ◽  
Gerben J. Zylstra
Keyword(s):  
Gene Knockout ◽  
Sole Source ◽  
Cleavage Product ◽  
Ring Cleavage ◽  
Catabolic Pathway ◽  
Double Knockout ◽  
Cleavage Enzyme ◽  
Sphingomonas Wittichii ◽  
Physiological Approach

Sphingomonas wittichii RW1 grows on the two related compounds dibenzofuran (DBF) and dibenzo- p -dioxin (DXN) as the sole source of carbon. Previous work by others (P.V. Bunz, R. Falchetto, and A.M. Cook. Biodegradation 4:171-8, 1993, doi: 10.1007/BF00695119) identified two upper pathway meta cleavage product hydrolases (DxnB1 and DxnB2) active on the DBF upper pathway metabolite 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate. We took a physiological approach to determine the role of these two enzymes in the degradation of DBF and DXN by RW1. Single knockouts of either plasmid located dbfB1 or chromosome located dbfB2 had no effect on RW1 growth on either DBF or DXN. However, a double knockout lost the ability to grow on DBF but still grew normally on DXN demonstrating that DbfB1 and DbfB2 are the only hydrolases involved in the DBF upper pathway. Using a transcriptomic-guided approach we identified a constitutively expressed third hydrolase encoded by the chromosomally located SWIT0910 gene. Knockout of SWIT0910 resulted in a strain that no longer grows on DXN but still grows normally on DBF. Thus the DbfB1 and DbfB2 hydrolases function in the DBF but not the DXN catabolic pathway and the SWIT0190 hydrolase functions in the DXN but not the DBF catabolic pathway. Importance S. wittichii RW1 is one of only a few strains known to grow on DXN as the sole course of carbon. Much of the work deciphering the related RW1 DXN and DBF catabolic pathways has involved genome gazing, transcriptomics, proteomics, heterologous expression, and enzyme purification and characterization. Very little research has utilized physiological techniques to precisely dissect the genes and enzymes involved in DBF and DXN degradation. Previous work by others identified and extensively characterized two RW1 upper pathway hydrolases. Our present work demonstrates that these two enzymes are involved in DBF but not DXN degradation. In addition, our work identified a third constitutively expressed hydrolase that is involved in DXN but not DBF degradation. Combined with our previous work, this means that the RW1 DXN upper pathway involves genes from three very different locations in the genome: an initial plasmid-encoded dioxygenase and a ring cleavage enzyme and hydrolase encoded on opposite sides of the chromosome.

Tryptophan Pyrrole Ring Cleavage Enzymes in Placenta

2003 ◽  
pp. 425-434 ◽  
Author(s):  
Yohsuke Minatogawa ◽  
Sachiko Suzuki ◽  
Yoko Ando ◽  
Shigenobu Tone ◽  
Osamu Takikawa
Keyword(s):  
Pyrrole Ring ◽  
Ring Cleavage

scholarly journals Key Aromatic-Ring-Cleaving Enzyme, Protocatechuate 3,4-Dioxygenase, in the Ecologically Important MarineRoseobacter Lineage

2000 ◽  
Vol 66 (11) ◽  
pp. 4662-4672 ◽  
Author(s):  
Alison Buchan ◽  
Lauren S. Collier ◽  
Ellen L. Neidle ◽  
Mary Ann Moran
Keyword(s):  
Aromatic Compounds ◽  
Southern Hybridization ◽  
Ring Cleavage ◽  
Degenerate Pcr ◽  
Cell Extracts ◽  
Aromatic Compound Degradation ◽  
Genes Encoding ◽  
Cleavage Enzyme ◽  
Key Enzyme ◽  
Dioxygenase Activity

ABSTRACT Aromatic compound degradation in six bacteria representing an ecologically important marine taxon of the α-proteobacteria was investigated. Initial screens suggested that isolates in theRoseobacter lineage can degrade aromatic compounds via the β-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. Six Roseobacter isolates were screened for the presence of protocatechuate 3,4-dioxygenase, a key enzyme in the β-ketoadipate pathway. All six isolates were capable of growth on at least three of the eight aromatic monomers presented (anthranilate, benzoate, p-hydroxybenzoate, salicylate, vanillate, ferulate, protocatechuate, and coumarate). Four of the Roseobacter group isolates had inducible protocatechuate 3,4-dioxygenase activity in cell extracts when grown onp-hydroxybenzoate. The pcaGH genes encoding this ring cleavage enzyme were cloned and sequenced from two isolates,Sagittula stellata E-37 and isolate Y3F, and in both cases the genes could be expressed in Escherichia coli to yield dioxygenase activity. Additional genes involved in the protocatechuate branch of the β-ketoadipate pathway (pcaC,pcaQ, and pobA) were found to cluster withpcaGH in these two isolates. Pairwise sequence analysis of the pca genes revealed greater similarity between the twoRoseobacter group isolates than between genes from eitherRoseobacter strain and soil bacteria. A degenerate PCR primer set targeting a conserved region within PcaH successfully amplified a fragment of pcaH from two additionalRoseobacter group isolates, and Southern hybridization indicated the presence of pcaH in the remaining two isolates. This evidence of protocatechuate 3,4-dioxygenase and the β-ketoadipate pathway was found in all six Roseobacterisolates, suggesting widespread abilities to degrade aromatic compounds in this marine lineage.

Degradation of phenanthrene and naphthalene by aBurkholderiaspecies strain

2003 ◽  
Vol 49 (2) ◽  
pp. 139-144 ◽  
Author(s):  
H Kang ◽  
S Y Hwang ◽  
Y M Kim ◽  
E Kim ◽  
Y -S Kim ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Energy Source ◽  
Enzyme Assay ◽  
Gas Chromatography Mass Spectrometry ◽  
Ring Cleavage ◽  
Growth Substrate ◽  
Degrading Bacteria ◽  
Subsequent Degradation ◽  
Cleavage Enzyme ◽  
Uv Visible

Burkholderia sp. TNFYE-5 was isolated from soil for the ability to grow on phenanthrene as sole carbon and energy source. Unlike most other phenanthrene-degrading bacteria, TNFYE-5 was unable to grow on naphthalene. Growth substrate range experiments coupled with the ring-cleavage enzyme assay data suggest that TNFYE-5 initially metabolizes phenanthrene to 1-hydroxy-2-naphthoate with subsequent degradation through the phthalate and protocatechuate and β-ketoadipate pathway. A metabolite in the degradation of naphthalene by TNFYE-5 was isolated by high-pressure liquid chromatography (HPLC) and was identified as salicylate by UV-visible spectral and gas chromatography – mass spectrometry analyses. Thus, the inability to degrade salicylate is apparently one major reason for the incapability of TNFYE-5 to grow on naphthalene.Key words: Burkholderia, phenanthrene, naphthalene, phthalate, protocatechuate.

Tryptophan 2,3-dioxygenase in Saccharomyces cerevisiae

1995 ◽  
Vol 41 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Yoshiki Iwamoto ◽  
In Sook Matsui Lee ◽  
Ryo Kido ◽  
Motonari Tsubaki
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Column Chromatography ◽  
Polyacrylamide Gel Electrophoresis ◽  
Ring Cleavage ◽  
Partial Purification ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cleavage Enzyme ◽  
A Subunit ◽  
Exogenous Ligands ◽  
Cellulose Column

The tryptophan pyrrole-ring cleavage enzyme (TPCE) was detected in the yeast Saccharomyces cerevisiae. TPCE activity existed constitutively and was markedly induced by culturing the cells in a medium containing 0.1% (w/v) L-tryptophan. We purified partially the enzyme from the L-tryptophan-induced cells by phospho-cellulose column chromatography. The partially purified enzyme was stimulated solely by L-ascorbic acid, a nonspecific reductant, suggesting that the yeast TPCE is not indoleamine 2,3-dioxygenase, but rather tryptophan 2,3-dioxygenase. The enzyme metabolized L-tryptophan preferentially, and D-tryptophan slightly. KCN and NaN3, exogenous ligands of heme, inhibited the enzyme activity drastically, indicating that yeast tryptophan 2,3-dioxygenase contains heme(s) in its active site. The optimal pH of the enzyme was 6.5. Upon two-dimensional polyacrylamide gel electrophoresis, a protein staining spot was identified that was induced by L-tryptophan and whose intensity changed in correlation with the tryptophan 2,3-dioxygenase activity after phospho-cellulose column chromatography. This protein, exhibiting a molecular weight of approximately 38 000 and an isoelectric point of approximately pH 8.0, may be identified as a subunit of yeast tryptophan 2,3-dioxygenase.Key words: tryptophan 2,3-dioxygenase, Saccharomyces cerevisiae, partial purification, heme.

scholarly journals Cloning of a Sphingomonas paucimobilis SYK-6 Gene Encoding a Novel Oxygenase That Cleaves Lignin-Related Biphenyl and Characterization of the Enzyme

1998 ◽  
Vol 64 (7) ◽  
pp. 2520-2527 ◽  
Author(s):  
Xue Peng ◽  
Takashi Egashira ◽  
Kaoru Hanashiro ◽  
Eiji Masai ◽  
Seiji Nishikawa ◽  
...  
Keyword(s):  
Cosmid Library ◽  
Ring Cleavage ◽  
Sphingomonas Paucimobilis ◽  
Class Iii ◽  
Extradiol Dioxygenase ◽  
Gene Encoding ◽  
Reading Frame ◽  
Yellow Color ◽  
Ring Fission ◽  
Cleavage Enzyme

ABSTRACT Sphingomonas paucimobilis SYK-6 transforms 2,2′-dihydroxy-3,3′-dimethoxy-5,5′-dicarboxybiphenyl (DDVA), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA) as an intermediate (15). The ring fission of OH-DDVA is an essential step in the DDVA degradative pathway. A 15-kbEcoRI fragment isolated from the cosmid library complemented the growth deficiency of a mutant on OH-DDVA. Subcloning and deletion analysis showed that a 1.4-kb DNA fragment included the gene responsible for the ring fission of OH-DDVA. An open reading frame encoding 334 amino acids was identified and designatedligZ. The deduced amino acid sequence of LigZ had 18 to 21% identity with the class III extradiol dioxygenase family, including the β subunit (LigB) of protocatechuate 4,5-dioxygenase of SYK-6 (Y. Noda, S. Nishikawa, K.-I. Shiozuka, H. Kadokura, H. Nakajima, K. Yano, Y. Katayama, N. Morohoshi, T. Haraguchi, and M. Yamasaki, J. Bacteriol. 172:2704–2709, 1990), catechol 2,3-dioxygenase I (MpcI) ofAlcaligenes eutrophus JMP222 (M. Kabisch and P. Fortnagel, Nucleic Acids Res. 18:3405–3406, 1990), the catalytic subunit of themeta-cleavage enzyme (CarBb) for 2′-aminobiphenyl-2,3-diol from Pseudomonas sp. strain CA10 (S. I. Sato, N. Ouchiyama, T. Kimura, H. Nojiri, H. Yamane, and T. Omori, J. Bacteriol. 179:4841–4849, 1997), and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB) ofEscherichia coli (E. L. Spence, M. Kawamukai, J. Sanvoisin, H. Braven, and T. D. H. Bugg, J. Bacteriol. 178:5249–5256, 1996). The ring fission product formed from OH-DDVA by LigZ developed a yellow color with an absorption maximum at 455 nm, suggesting meta cleavage. Thus, LigZ was concluded to be a ring cleavage extradiol dioxygenase. LigZ activity was detected only for OH-DDVA and 2,2′,3,3′-tetrahydroxy-5,5′-dicarboxybiphenyl and was dependent on the ferrous ion.

Evidence ThatpcpAEncodes 2,6-Dichlorohydroquinone Dioxygenase, the Ring Cleavage Enzyme Required for Pentachlorophenol Degradation inSphingomonas chlorophenolicaStrain ATCC 39723†

Biochemistry ◽  
1999 ◽  
Vol 38 (24) ◽  
pp. 7659-7669 ◽  
Author(s):  
Ling Xu ◽  
Katheryn Resing ◽  
Sherry L. Lawson ◽  
Patricia C. Babbitt ◽  
Shelley D. Copley
Keyword(s):  
Ring Cleavage ◽  
Cleavage Enzyme

A Novel Anthraquinone Ring Cleavage Enzyme from Aspergillus terreus

1988 ◽  
Vol 103 (5) ◽  
pp. 878-883 ◽  
Author(s):  
Isao Fujii ◽  
Yutaka Ebizuka ◽  
Ushio Sankawa
Keyword(s):  
Aspergillus Terreus ◽  
Ring Cleavage ◽  
Cleavage Enzyme

scholarly journals Identification of Genes Involved in Inversion of Stereochemistry of a C-12 Hydroxyl Group in the Catabolism of Cholic Acid by Comamonas testosteroni TA441

2008 ◽  
Vol 190 (16) ◽  
pp. 5545-5554 ◽  
Author(s):  
Masae Horinouchi ◽  
Toshiaki Hayashi ◽  
Hiroyuki Koshino ◽  
Michal Malon ◽  
Takako Yamamoto ◽  
...  
Keyword(s):  
Cholic Acid ◽  
Short Chain ◽  
Hydroxyl Group ◽  
Ring Cleavage ◽  
Comamonas Testosteroni ◽  
Enzyme Gene ◽  
Acid Degradation ◽  
Cleavage Enzyme ◽  
Short Chain Dehydrogenase

ABSTRACT Comamonas testosteroni TA441 degrades steroids such as testosterone via aromatization of the A ring, followed by meta-cleavage of the ring. In the DNA region upstream of the meta-cleavage enzyme gene tesB, two genes required during cholic acid degradation for the inversion of an α-oriented hydroxyl group on C-12 were identified. A dehydrogenase, SteA, converts 7α,12α-dihydroxyandrosta-1,4-diene-3,17-dione to 7α-hydroxyandrosta-1,4-diene-3,12,17-trione, and a hydrogenase, SteB, converts the latter to 7α,12β-dihydroxyandrosta-1,4-diene-3,17-dione. Both enzymes are members of the short-chain dehydrogenase/reductase superfamily. The transformation of 7α,12α-dihydroxyandrosta-1,4-diene-3,17-dione to 7α,12β-dihydroxyandrosta-1,4-diene-3,17-dione is carried out far more effectively when both SteA and SteB are involved together. These two enzymes are encoded by two adjacent genes and are presumed to be expressed together. Inversion of the hydroxyl group at C-12 is indispensable for the subsequent effective B-ring cleavage of the androstane compound. In addition to the compounds already mentioned, 12α-hydroxyandrosta-1,4,6-triene-3,17-dione and 12β-hydroxyandrosta-1,4,6-triene-3,17-dione were identified as minor intermediate compounds in cholic acid degradation by C. testosteroni TA441.

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