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Sgro M, Chow N, Olyaei F, Arentshorst M, Geoffrion N, Ram AFJ, Powlowski J, Tsang A. Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger. J Biol Chem 2023; 299:105003. [PMID: 37399977 PMCID: PMC10406623 DOI: 10.1016/j.jbc.2023.105003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl-CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate.
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Affiliation(s)
- Michael Sgro
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Nicholas Chow
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Farnaz Olyaei
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
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Degradation of cinnamic acid by a newly isolated bacterium Stenotrophomonas sp. TRMK2. 3 Biotech 2018; 8:368. [PMID: 30105193 DOI: 10.1007/s13205-018-1390-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022] Open
Abstract
A bacterium Stenotrophomonas sp. TRMK2 capable of utilizing cinnamic acid was isolated from agro-industrial waste by enrichment culture technique. This strain completely utilizes 5 mM cinnamic acid within 18 h of incubation. The different metabolites formed during the degradation of cinnamic acid were characterized by GC-HRMS. The involvement of various enzymes, namely cinnamate reductase, 3-phenylpropionic acid hydroxylase, p-hydroxybenzoic acid hydroxylase and protocatechuate 3,4-dioxygenase in cinnamic acid degradation was demonstrated. A catabolic pathway for cinnamic acid in Stenotrophomonas sp. TRMK2 is as follows: Cinnamic acid; 3-Phenylpropionic acid; 3-(4-Hydroxyphenyl) propionic acid; 4-Hydroxy benzoic acid and Protocatechuic acid. Further, this strain is capable of utilizing various phenolic compounds.
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3
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Biodegradation of fluoranthene by Paenibacillus sp. strain PRNK-6: a pathway for complete mineralization. Arch Microbiol 2017; 200:171-182. [DOI: 10.1007/s00203-017-1431-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/04/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
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T R M, I M, B K, Reddy PV, Nayak AS, Karegoudar TB. Utilization of Phenylpropanoids by Newly Isolated Bacterium Pseudomonas sp. TRMK1. Appl Biochem Biotechnol 2017; 182:1240-1255. [DOI: 10.1007/s12010-017-2396-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
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5
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Harrington LB, Jha RK, Kern TL, Schmidt EN, Canales GM, Finney KB, Koppisch AT, Strauss CEM, Fox DT. Rapid Thermostabilization of Bacillus thuringiensis Serovar Konkukian 97-27 Dehydroshikimate Dehydratase through a Structure-Based Enzyme Design and Whole Cell Activity Assay. ACS Synth Biol 2017; 6:120-129. [PMID: 27548779 DOI: 10.1021/acssynbio.6b00159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermostabilization of an enzyme with complete retention of catalytic efficiency was demonstrated on recombinant 3-dehydroshikimate dehydratase (DHSase or wtAsbF) from Bacillus thuringiensis serovar konkukian 97-27 (hereafter, B. thuringiensis 97-27). The wtAsbF is relatively unstable at 37 °C, in vitro (t1/237 = 15 min), in the absence of divalent metal. We adopted a structure-based design to identify stabilizing mutations and created a combinatorial library based upon predicted mutations at specific locations on the enzyme surface. A diversified asbF library (∼2000 variants) was expressed in E. coli harboring a green fluorescent protein (GFP) reporter system linked to the product of wtAsbF activity (3,4-dihydroxybenzoate, DHB). Mutations detrimental to DHSase function were rapidly eliminated using a high throughput fluorescence activated cell sorting (FACS) approach. After a single sorting round and heat screen at 50 °C, a triple AsbF mutant (Mut1), T61N, H135Y, and H257P, was isolated and characterized. The half-life of Mut1 at 37 °C was >10-fold higher than the wtAsbF (t1/237 = 169 min). Further, the second-order rate constants for both wtAsbF and Mut1 were approximately equal (9.9 × 105 M-1 s-1, 7.8 × 105 M-1 s-1, respectively), thus demonstrating protein thermostability did not come at the expense of enzyme thermophilicity. In addition, in vivo overexpression of Mut1 in E. coli resulted in a ∼60-fold increase in functional enzyme when compared to the wild-type enzyme under the identical expression conditions. Finally, overexpression of the thermostable AsbF resulted in an approximate 80-120% increase in DHB accumulation in the media relative to the wild-type enzyme.
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Affiliation(s)
- Lucas B. Harrington
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Ramesh K. Jha
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Theresa L. Kern
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Emily N. Schmidt
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - Gustavo M. Canales
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Kellan B. Finney
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Andrew T. Koppisch
- Department
of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86001, United States
| | - Charlie E. M. Strauss
- Bioscience
Division, Los Alamos National Laboratory, P.O. Box 1663, MS M888, Los Alamos, New Mexico 87545, United States
| | - David T. Fox
- Chemistry
Division, Los Alamos National Laboratory, P.O. Box 1663, MS E554, Los Alamos, New Mexico 87545, United States
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6
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Biodegradation of synthetic pyrethroids by Ochrobactrum tritici strain pyd-1. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0698-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Metabolic production of a novel polymer feedstock, 3-carboxy muconate, from vanillin. Appl Microbiol Biotechnol 2011; 90:107-16. [DOI: 10.1007/s00253-010-3078-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 12/14/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
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8
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Prathibha K, Sumathi S. Biodegradation of mixture containing monohydroxybenzoate isomers by Acinetobacter calcoaceticus. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9545-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Tallur PN, Megadi VB, Ninnekar HZ. Biodegradation of Cypermethrin by Micrococcus sp. strain CPN 1. Biodegradation 2007; 19:77-82. [PMID: 17431802 DOI: 10.1007/s10532-007-9116-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 03/27/2007] [Indexed: 11/28/2022]
Abstract
A bacterium capable of utilizing pyrethroid pesticide cypermethrin as sole source of carbon was isolated from soil and identified as a Micrococcus sp. The organism also utilized fenvalerate, deltamethrin, perimethrin, 3-phenoxybenzoate, phenol, protocatechuate and catechol as growth substrates. The organism degraded cypermethrin by hydrolysis of ester linkage to yield 3-phenoxybenzoate, leading to loss of its insecticidal activity. 3-Phenoxybenzoate was further metabolized by diphenyl ether cleavage to yield protocatechuate and phenol as evidenced by isolation and identification of metabolites and enzyme activities in the cell-free extracts. Protocatechuate and phenol were oxidized by ortho-cleavage pathway. Thus, the organism was versatile in detoxification and complete mineralization of pyrethroid cypermethrin.
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Affiliation(s)
- Preeti N Tallur
- Department of Biochemistry, Karnataka University, Dharwad 580003, India
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Patil NK, Kundapur R, Shouche YS, Karegoudar TB. Degradation of Plasticizer Di-n-butylphthalate by Delftia sp. TBKNP-05. Curr Microbiol 2006; 52:369-74. [PMID: 16604416 DOI: 10.1007/s00284-005-5258-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 11/03/2005] [Indexed: 10/24/2022]
Abstract
Bacterial strain Delftia sp. TBKNP-05, isolated by para-hydroxybenzoate enrichment technique, is capable of degrading di-n-butylphthalate (DBP) as a sole source of carbon and energy. Analysis of intermediates by thin-layer chromatography and high-performance liquid chromatography indicated the presence of monobutylphthalate (MBP), phthalate (PA), and protocatechuate (PCA). The washed cells grown on DBP and PA showed appreciable oxidation of DBP, MBP, PA, and PCA. The enzyme activities in cell-free extracts of Delftia sp. TBKNP-05 exhibited the presence of DBP esterase, MBP esterase, PA-dioxygenase, and PCA 4,5-dioxygenase. The PCA is metabolized by meta-cleavage pathway, leading to further mineralization of the compound in this bacterium.
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11
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Patil NK, Kundapur R, Shouche YS, Karegoudar TB. Degradation of a Plasticizer, di-n-Butylphthalate by Delftia sp. TBKNP-05. Curr Microbiol 2006; 52:225-30. [PMID: 16502295 DOI: 10.1007/s00284-005-0258-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 11/03/2005] [Indexed: 11/29/2022]
Abstract
A bacterial strain Delftia sp. TBKNP-05 isolated by para-hydroxybenzoate enrichment technique is capable of degrading di-n-butylphthalate (DBP) as a sole source of carbon and energy. Analysis of intermediates by thin layer chromatography and high performance liquid chromatography indicated the presence of monobutylphthalate (MBP), phthalate (PA), and protocatechuate (PCA). The washed cells grown on DBP and PA showed appreciable oxidation of DBP, MBP, PA, and PCA. The enzyme activities in cell free extracts of Delftia sp. TBKNP-05 exhibited the presence of DBP esterase, MBP esterase, PA-dioxygenase, and protocatechuate 4, 5-dioxygenase. The protocatechuate is metabolized by a meta-cleavage pathway leading to further mineralization of the compound in this bacterium.
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12
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Goren MB, Sokoloski EA, Fales HM. 2-Methyl-(1 Z,3 E)-butadiene-1,3,4-tricarboxylic Acid, “Isoprenetricarboxylic Acid”. J Org Chem 2005; 70:7429-31. [PMID: 16122270 DOI: 10.1021/jo0507892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The synthesis of the title compound 7 from ethyl glyoxylate and dimethyl and diethyl beta-methylglutaconate is described along with its physical properties that suggest its inability to assume a cis-dienoid structure due to steric hindrance between the methyl and carboxyl groups.
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Affiliation(s)
- Mayer B Goren
- Laboratory of Applied Mass Spectrometry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA
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13
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Shimoni E, Baasov T, Ravid U, Shoham Y. The trans-anethole degradation pathway in an Arthrobacter sp. J Biol Chem 2002; 277:11866-72. [PMID: 11805095 DOI: 10.1074/jbc.m109593200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A bacterial strain (TA13) capable of utilizing t-anethole as the sole carbon source was isolated from soil. The strain was identified as Arthrobacter aurescens based on its 16 S rRNA gene sequence. Key steps of the degradation pathway of t-anethole were identified by the use of t-anethole-blocked mutants and specific inducible enzymatic activities. In addition to t-anethole, strain TA13 is capable of utilizing anisic acid, anisaldehyde, and anisic alcohol as the sole carbon source. t-Anethole-blocked mutants were obtained following mutagenesis and penicillin enrichment. Some of these blocked mutants, accumulated in the presence of t-anethole quantitative amounts of t-anethole-diol, anisic acid, and 4,6-dicarboxy-2-pyrone and traces of anisic alcohol and anisaldehyde. Enzymatic activities induced by t-anethole included: 4-methoxybenzoate O-demethylase, p-hydroxybenzoate 3-hydroxylase, and protocatechuate-4,5-dioxygenase. These findings indicate that t-anethole is metabolized to protocatechuic acid through t-anethole-diol, anisaldehyde, anisic acid, and p-hydroxybenzoic acid. The protocatechuic acid is then cleaved by protocatechuate-4,5-dioxygenase to yield 2-hydroxy-4-carboxy muconate-semialdehyde. Results from inducible uptake ability and enzymatic assays indicate that at least three regulatory units are involved in the t-anethole degradation pathway. These findings provide new routes for environmental friendly production processes of valuable aromatic chemicals via bioconversion of phenylpropenoids.
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Affiliation(s)
- Eyal Shimoni
- Department of Food Engineering and Biotechnology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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14
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Affiliation(s)
- J L Ingraham
- Section of Microbiology, Emeritus, University of California, Davis, California 95616, USA.
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15
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DAGLEY S, EVANS WC, RIBBONS DW. New pathways in the oxidative metabolism of aromatic compounds by microorganisms. Nature 1998; 188:560-6. [PMID: 13719300 DOI: 10.1038/188560a0] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Frazee RW, Orville AM, Dolbeare KB, Yu H, Ohlendorf DH, Lipscomb JD. The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates. Biochemistry 1998; 37:2131-44. [PMID: 9485360 DOI: 10.1021/bi972047b] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The essential active site Fe3+ of protocatechuate 3,4-dioxygenase [3, 4-PCD, subunit structure (alphabetaFe3+)12] is bound by axial ligands, Tyr447 (147beta) and His462 (162beta), and equatorial ligands, Tyr408 (108beta), His460 (160beta), and a solvent OH- (Wat827). Recent X-ray crystallographic studies have shown that Tyr447 is dissociated from the Fe3+ in the anaerobic 3,4-PCD complex with protocatechuate (PCA) [Orville, A. M., Lipscomb, J. D., and Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066]. The importance of Tyr447 to catalysis is investigated here by site-directed mutation of this residue to His (Y447H), the first such mutation reported for an aromatic ring cleavage dioxygenase containing Fe3+. The crystal structure of Y447H (2.1 A resolution, R-factor of 0.181) is essentially unchanged from that of the native enzyme outside of the active site region. The side chain position of His447 is stabilized by a His447(N)delta1-Pro448(O) hydrogen bond, placing the Nepsilon2 atom of His447 out of bonding distance of the iron ( approximately 4.3 A). Wat827 appears to be replaced by a CO32-, thereby retaining the overall charge neutrality and coordination number of the Fe3+ center. Quantitative metal and amino acid analysis shows that Y447H binds Fe3+ in approximately 10 of the 12 active sites of 3,4-PCD, but its kcat is nearly 600-fold lower than that of the native enzyme. Single-turnover kinetic analysis of the Y447H-catalyzed reaction reveals that slow substrate binding accounts for the decreased kcat. Three new kinetically competent intermediates in this process are revealed. Similarly, the product dissociation from Y447H is slow and occurs in two resolved steps, including a previously unreported intermediate. The final E.PCA complex (ES4) and the putative E.product complex (ESO2*) are found to have optical spectra that are indistinguishable from those of the analogous intermediates of the wild-type enzyme cycle, while all of the other observed intermediates have novel spectra. Once the E.S complex is formed, reaction with O2 is fast. These results suggest that dissociation of Tyr447 occurs during turnover of 3,4-PCD and is important in the substrate binding and product release processes. Once Tyr447 is removed from the Fe3+ in the final E.PCA complex by either dissociation or mutagenesis, the O2 attack and insertion steps proceed efficiently, suggesting that Tyr447 does not have a large role in this phase of the reaction. This study demonstrates a novel role for Tyr in a biological system and allows evaluation and refinement of the proposed Fe3+ dioxygenase mechanism.
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Affiliation(s)
- R W Frazee
- Department of Biochemistry, Medical School, and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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17
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DAGLEY S, CHAPMAN PJ, GIBSON DT, WOOD JM. DEGRADATION OF THE BENZENE NUCLEUS BY BACTERIA. Nature 1996; 202:775-8. [PMID: 14187616 DOI: 10.1038/202775a0] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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19
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Contzen M, Wittich RM, Knackmuss HJ, Stolz A. Degradation of benzene 1,3-disulfonate by a mixed bacterial culture. FEMS Microbiol Lett 1996. [DOI: 10.1111/j.1574-6968.1996.tb08023.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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20
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Abstract
Aspergillus niger (AG-1) metabolized dimethylterephthalate through monomethylterephthalate, terephthalate and protocatechuate. Degradation of dimethylterephthalate was followed by extraction of residual dimethylterephthalate from the spent medium. The quantitative UV analysis showed that 58% of the dimethylterephthalate supplement was taken up in 144 h. The metabolites were isolated from resting cell cultures. Thin layer chromatography analysis of the extract revealed the presence of two intermediates, monomethylterephthalate and terephthalate. Use of an inhibitor in resting cell culture experiment demonstrated the accumulation of protocatechuate. The time course of protocatechuate accumulation was also studied. Metabolites were identified by employing various physicochemical methods. Enzyme studies using cell-free extracts exhibited dimethylterephthalate esterase and protocatechuate dioxygenase activities. Protocatechuate was oxidized by the meta cleavage pathway. A tentative pathway for the degradation of DMTP has been proposed in A. niger.
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Affiliation(s)
- S H Ganji
- Department of Chemistry, Karnatak University, Dharwad, India
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21
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Feigel BJ, Knackmuss HJ. Syntrophic interactions during degradation of 4-aminobenzenesulfonic acid by a two species bacterial culture. Arch Microbiol 1993; 159:124-30. [PMID: 8439234 DOI: 10.1007/bf00250271] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
During synthrophic growth of Hydrogenophaga palleronii (strain S1) and Agrobacterium radiobacter (strain S2) with 4-aminobenzene sulfonate (4ABS) only strain S1 desaminates 4ABS by regioselective 3,4-dioxygenation. The major part of the metabolite catechol-4-sulfonate (4CS) is excreted and further metabolized by strain S2. Although both organisms harbour activities of protocatechuate pathways assimilation of the structural analog 4CS requires first of all enzyme activities with broader substrate specificity: protocatechuate 3,4-dioxygenase and carboxymuconate cycloisomerase activities were identified which in addition to the natural substrates also convert 4CS and 3-sulfomuconate respectively. 4-Carboxymethyl-4-sulfobut-2-en-4-olide (4SL) was identified as a metabolite. Its further metabolism requires a desulfonating enzyme which eliminates sulfite from (4SL) and generates maleylacetate. Convergence with the 3-oxoadipate pathway is catalyzed by a maleyl acetate reductase, which was identified in cell-free extracts of both organisms S1 and S2. Characteristically, only strain S1 can oxidize sulfite and thus contributes to the interdependence of the two bacteria during growth with 4ABS.
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Affiliation(s)
- B J Feigel
- Institut für Mikrobiologie, Universität Stuttgart, Federal Republic of Germany
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22
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Albro PW, Corbett JT, Schroeder JL. The metabolism of di(2-ethylhexyl)phthalate in the earthworm Lumbricus terrestris. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. C, COMPARATIVE PHARMACOLOGY AND TOXICOLOGY 1993; 104:335-44. [PMID: 8098688 DOI: 10.1016/0742-8413(93)90045-m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
1. Earthworms can hydrolyze di-(2-ethylhexyl) phthalate (DEHP) to mono-2-ethylhexyl phthalate (MEHP) and phthalic acid (PA). 2. They apparently cannot produce the side-chain-oxidized derivatives of MEHP that constitute the major DEHP metabolites in higher animals. 3. With the assistance of intestinal bacterial Pseudomonas, the worm-derived PA is degraded through protocatechuic and beta-carboxymuconic acids to CO2. 4. There is an indication of a second pathway for degradation of PA leading through benzoic acid.
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Affiliation(s)
- P W Albro
- Laboratory of Molecular Biophysics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
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Whited GM, Gibson DT. Separation and partial characterization of the enzymes of the toluene-4-monooxygenase catabolic pathway in Pseudomonas mendocina KR1. J Bacteriol 1991; 173:3017-20. [PMID: 2019564 PMCID: PMC207886 DOI: 10.1128/jb.173.9.3017-3020.1991] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The route of toluene degradation by Pseudomonas mendocina KR1 was studied by separating or purifying from toluene-grown cells the catabolic enzymes responsible for oxidation of p-cresol through the ring cleavage step. Enzymatic transformations corresponding to each of the metabolic steps in the proposed degradative pathway were conducted with cell-free preparations. p-Cresol was metabolized by the enzyme p-cresol methylhydroxylase to p-hydroxybenzaldehyde. p-Hydroxybenzaldehyde was further oxidized by partially purified enzyme preparations to p-hydroxybenzoate and subsequently hydroxylated to form protocatechuate. Protocatechuate was then oxidized by ortho ring cleavage.
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Affiliation(s)
- G M Whited
- Center for Applied Microbiology, University of Texas, Austin 78712
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Trias J, Viñas M, Guinea J, Lorén JG. Induction of Yellow Pigmentation in
Serratia marcescens. Appl Environ Microbiol 1988; 54:3138-41. [PMID: 16347803 PMCID: PMC204439 DOI: 10.1128/aem.54.12.3138-3141.1988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The appearance of yellow pigmentation in nonpigmented strains of
Serratia
sp. has been demonstrated to be due to the production of a muconic acid, 2-hydroxy-5-carboxymethylmuconic acid semialdehyde. The 3,4-dihydroxyphenylacetate 2,3-dioxygenase responsible for the synthesis of this muconic acid was induced in all strains tested. Another muconic acid, the β-
cis-cis
-carboxymuconic acid, could also be synthesized from 3,4-dihydroxybenzoate, but this product was not colored. Mutants that were unable to grow on tyrosine and produced yellow pigment were isolated from nonpigmented strains. These mutants had properties similar to those of the yellow-pigmented strains. The ability to produce pigment may be more widespread among
Serratia marcescens
strains than is currently known.
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Affiliation(s)
- J Trias
- Departament de Microbiologia i Parasitologia Sanitàries, Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Spain
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25
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The involvement of an enantioselective transaminase in the metabolism of D-3- and D-4-hydroxyphenylglycine inPseudomonas putida LW-4. Appl Microbiol Biotechnol 1988. [DOI: 10.1007/bf01982906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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The involvement of an enantioselective transaminase in the metabolism of D-3- and D-4-hydroxyphenylglycine in Pseudomonas putida LW-4. Appl Microbiol Biotechnol 1988. [DOI: 10.1007/bf00251706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Wojta?-Wasilewska M, Luterek J, Leonowicz A, Dawidowicz A. Dearomatization of lignin derivatives by fungal protocatechuate 3,4-dioxygenase immobilized on porosity glass. Biotechnol Bioeng 1988; 32:507-11. [DOI: 10.1002/bit.260320413] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Abstract
Micrococcus sp. strain 12B was isolated by enriching for growth with dibutylphthalate as the sole carbon and energy source. A pathway for the metabolism of dibutylphthalate and phthalate by micrococcus sp. strain 12B is proposed: dibutylphthalate leads to monobutylphthalate leads to phthalate leads to 3,4-dihydro-3,4-dihydroxyphthalate leads to 3,4-dihydroxyphthalate leads to protocatechuate (3,4-dihdroxybenzoate). Protocatechuate is metabolized both by the meta-cleavage pathway through 4-carboxy-2-hydroxymuconic semialdehyde and 4-carboxy-2-hydroxymuconate to pyruvate and oxaloacetate and by the ortho-cleavage pathway to beta-ketoadipate. Dibutylphthalate- and phthalate-grown cells readily oxidized dibutylphthalate, phthalate, 3,4-dihydroxyphthalate, and protocatechuate. Extracts of cells grown with dibutylphthalate or phthalate contained the 3,4-dihydroxyphthalate decarboxylase and the enzymes of the protocatechuater 4,5-meta-cleavage pathway. Extracts of dibutylphthalate-grown cells also contained the protocatechuate ortho-cleavage pathway enzymes. The dibutylphthalate-hydrolyzing esterase and 3,4-dihydroxyphthalate decarboxylase were constitutively synthesized; phthalate-3,4-dioxygenase (and possibly the "dihydrodiol" dehydrogenase) was inducible by phthalate or a metabolite occurring before protocatechuate in the pathway; two protocatechuate oxygenases and subsequent enzymes were inducible by protocatechuate or a subsequent metabolic product. During growth at 37 degrees C, strain 12B gave clones at high frequency that had lost the ability to grow with phthalate esters. One of these nonrevertible mutants, strain 12B-Cl, lacked all of the enzymes required for the metabolism of dibutylphthalate through the protocatechuate meta-cleavage pathway. Enzymes for the metabolism of protocatechuate by the ortho-cleavage pathway were present in this strain grown with p-hydroxybenzoate or protocatechuate.
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30
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Bull C, Ballou D. Purification and properties of protocatechuate 3,4-dioxygenase from Pseudomonas putida. A new iron to subunit stoichiometry. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(18)42947-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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31
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Sutherland JB, Crawford DL, Pometto AL. Catabolism of Substituted Benzoic Acids by
Streptomyces
Species. Appl Environ Microbiol 1981; 41:442-8. [PMID: 16345718 PMCID: PMC243713 DOI: 10.1128/aem.41.2.442-448.1981] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four thermotolerant actinomycetes from soil, identified as
Streptomyces albulus
321,
Streptomyces sioyaensis
P5,
Streptomyces viridosporus
T7A, and
Streptomyces
sp. V7, were grown at 45°C in media containing either benzoic acid or hydroxyl- and methoxyl-substituted benzoic acids as the principal carbon sources. Benzoic acid was converted to catechol;
p
-hydroxybenzoic, vanillic, and veratric acids were converted to protocatechuic acid; and
m
-hydroxybenzoic acid was converted to gentisic acid. Catechol, protocatechuic acid, and gentisic acid were cleaved by catechol 1,2-dioxygenase, protocatechuate 3,4-dioxygenase, and gentisate 1,2-dioxygenase, respectively. Dioxygenases appeared only in induced cultures.
m
-Hydroxybenzoic,
m
-anisic, and
p
-anisic acids were gratuitous inducers of dioxygenases in some strains. One strain converted vanillic acid to guaiacol.
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Affiliation(s)
- J B Sutherland
- Department of Bacteriology and Biochemistry, Idaho Agricultural Experiment Station, University of Idaho, Moscow, Idaho 83843
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32
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Mohan V, Kishore G, Sugumaran M, Vaidyanathan C. Purification and properties of protocatechuate-3,4-dioxygenase from Tecoma stans L. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/0304-4211(79)90037-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Parke D. Structural comparison of gamma-carboxymuconolactone decarboxylase and muconolactone isomerase from Pseudomonas putida. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 578:145-54. [PMID: 454663 DOI: 10.1016/0005-2795(79)90122-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Saito K, Komamine A. Biosynthesis of stizolobinic acid and stizolobic acid in higher plants. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:385-92. [PMID: 624278 DOI: 10.1111/j.1432-1033.1978.tb12033.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Hou CT. Iron-binding ligands in the catalytic site of protocatechuate 3,4-dioxygenase. BIOINORGANIC CHEMISTRY 1978; 8:237-43. [PMID: 647056 DOI: 10.1016/s0006-3061(00)80199-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The tryptophan fluorescence maximum for holoprotocatechuate 3,4-dioxygenase(holo PCD) is blue-shifted slightly (3 nm) from that of the apoenzyme. In the preparation of apoenzyme, increases in tryptophan fluorescence intensity coincided with decreases in enzyme activity and decreases in iron content. The tryptophan emission intensity of reconstituted enzyme having full enzyme activity was about 90% of that of the holoenzyme. Although apo PCD has similar molecular weight, amino acid content and essentially the same gross quaternary conformation as holo PCD, the absence of iron in apo PCD causes the changes in emission intensity of tryptophan. Findings indicate that some tryptophan residues may be (or may be near) the iron-binding ligands in the catalytic site of protocatechuate 3,4-dioxygenase.
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36
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Hou CT, Lillard MO. Immunological properties of protocatechuate 3, 4-dioxygenase isofunctional enzymes. J Bacteriol 1976; 126:516-9. [PMID: 816780 PMCID: PMC233308 DOI: 10.1128/jb.126.1.516-519.1976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antiserum prepared against protocatechuate 3, 4-dioxygenase from Pseudomonas aeruginosa forms precipitin bands without spurs with isofunctional enzymes from different strains of the fluorescent pseudomonads on immunodiffusion plates. Catalytic activity of the isofunctional enzymes was inhibited by an immunoglobulin fraction prepared against the enzyme from organisms of the same genus and not from different genera.
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37
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Sharma HK, Vaidyanathan CS. A new mode of ring cleavage of 2,3-dihydroxybenzoic acid in Tecoma stans (L.). Partial purification and properties of 2,3-dihydroxybenzoate 2,3-oxygenase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 56:163-71. [PMID: 1175620 DOI: 10.1111/j.1432-1033.1975.tb02219.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2,3-Dihydroxybenzoic acid has been shown to be oxidized via the 3-oxoadipate pathway in the leaves of Tecoma stans. The formation of 2-carboxy-cis,cis-muconic acid, a muconolactone, 3-oxoadipic acid and carbon dioxide during its metabolism has been demonstrated using an extract of Tecoma leaves. The first reaction of the pathway, viz., the conversion of 2,3-dihydroxybenzoate to 2-carboxy-cis,cis-muconic acid has been shown to be catalysed by an enzyme designated as 2,3-dihydroxybenzoate 2,3-oxygenase. The enzyme has been partially purified and a few of its properties studied. The enzyme is very labile with a half-life of 3--4 h. It is maximally active with 2,3-dihydroxybenzoate as the substrate and does not exhibit any activity with catechol, 4-methyl catechol, 3,4-dihydroxybenzoic acid, etc. However, 2,3-dihydroxy-p-toluate and 2,3-dihydroxy-p-cumate are also oxidized by the enzyme by about 38% and 28% respectively, compared to 2,3-dihydroxybenzoate. Sulfhydryl reagents inhibit the enzyme reaction and the inhibition can be prevented by preincubation of the enzyme with the substrate. Substrate also affords protection to the enzyme against thermal inactivation. Sulfhydryl compounds strongly inhibit the reaction and the inhibition cannot be prevented by preincubation of the enzyme with its substrates. Data on the effect of metal ions as well as metal chelating agents suggest that copper is the metal cofactor of the enzyme. Evidence is presented which suggests that iron may not be participating in the overall catalytic mechanism.
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38
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Fujisawa H, Uyeda M. Protocatechuate 3, 4-dioxygenase. Cobalt substitution for iron. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 45:223-31. [PMID: 4371338 DOI: 10.1111/j.1432-1033.1974.tb03546.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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39
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40
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Meagher RB, McCorkle GM, Ornston MK, Ornston LN. Inducible uptake system for -carboxy-cis, cis-muconate in a permeability mutant of Pseudomonas putida. J Bacteriol 1972; 111:465-73. [PMID: 5053469 PMCID: PMC251306 DOI: 10.1128/jb.111.2.465-473.1972] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A procedure for the large-scale enzymatic synthesis of beta-carboxymuconate is described. When used as a growth substrate, beta-carboxymuconate selected for mutant strains of Pseudomonas putida that were permeable to polycarboxylic acid intermediates of the beta-ketoadipate pathway. One mutant organism, strain PRS2110, was investigated in detail. It differed from the parental strain in that it possessed a beta-carboxymuconate uptake system that was formed when the compound was supplied exogenously to the cells. The uptake system was not induced by beta-carboxymuconate supplied endogenously during growth with p-hydroxybenzoate. These observations suggested that beta-carboxymuconate was contained within a physical compartment of enzymes during growth with p-hydroxybenzoate. Support for this hypothesis came from the demonstration that enzymes of the beta-ketoadipate pathway were held together by weak chemical interactions during the chromatography of crude extracts of benzoategrown P. putida on diethylaminoethyl-cellulose columns.
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41
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42
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Fujisawa H, Hiromi K, Uyeda M, Okuno S, Nozaki M, Hayaishi O. Protocatechuate 3,4-Dioxygenase. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)45089-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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43
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Buswell JA, Mahmood A. Bacterial degradation of p-methoxybenzoic acid. ARCHIV FUR MIKROBIOLOGIE 1972; 84:275-86. [PMID: 4403322 DOI: 10.1007/bf00409077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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44
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Teng N, Kotowycz G, Calvin M, Hosokawa K. Mechanism of Action of p-Hydroxybenzoate Hydroxylase from Pseudomonas putida. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)61927-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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45
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46
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47
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Seidman MM, Toms A, Wood JM. Influence of side-chain substituents on the position of cleavage of the benzene ring by Pseudomonas fluorescens. J Bacteriol 1969; 97:1192-7. [PMID: 5776526 PMCID: PMC249834 DOI: 10.1128/jb.97.3.1192-1197.1969] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Pseudomonas fluorescens was grown on mineral salts media with phenol, p-hydroxybenzoic acid, p-hydroxy-phenylacetic acid, or p-hydroxy-trans-cinnamic acid as sole carbon and energy source. Each compound was first hydroxylated, ortho to the hydroxyl group on the benzene ring, to give catechol, protocatechuic acid (3,4-dihydroxy-benzoic acid), homoprotocatechuic acid (3,4-dihydroxy-phenylacetic acid), and caffeic acid (3,4-dihydroxy-trans-cinnamic acid), respectively, as the ultimate aromatic products before cleavage of the benzene nucleus. Protocatechuic acid and caffeic acid were shown to be cleaved by ortho fission, via a 3,4-oxygenase mechanism, to give beta-substituted cis, cis-muconic acids as the initial aliphatic products. However, catechol and homoprotocatechuic acid were cleaved by meta fission, by 2,3-and 4,5-oxygenases, respectively, to give alpha-hydroxy-muconic semialdehyde and alpha-hydroxy-gamma-carboxymethyl muconic semialdehyde as initial aliphatic intermediates. Caffeic acid: 3,4-oxygenase, a new oxygenase, consumes 1 mole of O(2) per mole of substrate and has an optimal pH of 7.0. The mechanism of cleavage of enzymes derepressed for substituted catechols by P. fluorescens apparently changes from ortho to meta with the increasing nephelauxetic (electron donor) effect of the side-chain substituent.
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48
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49
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Gibson DT, Wood JM, Chapman PJ, Dagley S. Bacterial degradation of aromatic compounds. Biotechnol Bioeng 1967. [DOI: 10.1002/bit.260090105] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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50
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Humphrey AE. A critical review of hydrocarbon fermentations and their industrial utilization. Biotechnol Bioeng 1967. [DOI: 10.1002/bit.260090103] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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