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MetaCyc Pathway: 2-hydroxybiphenyl degradation
Traceable author statement to experimental supportInferred from experiment

Pathway diagram: 2-hydroxybiphenyl degradation

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationAromatic Compounds Degradation

Some taxa known to possess this pathway include : Pseudomonas nitroreducens

Expected Taxonomic Range: Bacteria

General Background

This background summary covers this pathway and related pathways 2,2'-dihydroxybiphenyl degradation, 2-propylphenol degradation and 2-isopropylphenol degradation. These pathways were studied in Pseudomonas nitroreducens, or a regulatory mutant of Pseudomonas nitroreducens designated Prp, as described below.

This pathway: 2-hydroxybiphenyl has been used as a volatile fungicide (in [Kohler93]) and is a product of dibenzothiophene desulfurization (in [Suske97]). Pseudomonas nitroreducens (previously known as Pseudomonas azelaica HBP1 or Pseudomonas sp. strain HBP1) was able to grow on 2-hydroxybiphenyl as a sole source of carbon and energy via a pathway involving ortho hydroxylation by a soluble, NADH-dependent monooxygenase (HbpA), ring cleavage of the hydroxylated product at the meta position by a dioxygenase (HbpC), and hydrolysis of the meta cleavage product by a hydrolase (HbpD) to produce benzoate and the common aromatic intermediate 2-oxopent-4-enoate (which has an enol tautomeric form (2E)-2-hydroxypenta-2,4-dienoate). The latter two compounds were further metabolized as shown in the pathway links. The last two reactions of this pathway are shared with pathway biphenyl degradation ( [Kohler88, Kohler93] and in [Jaspers00]).

Pathway 2,2'-dihydroxybiphenyl degradation: Pseudomonas nitroreducens was also able to grow on 2,2'-dihydroxybiphenyl as a sole source of carbon and energy via enzymes HbpA, HbpC and HbpD, producing the intermediates 2,2',3-trihydroxybiphenyl, (2Z,2E)-2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate, salicylate, and 2-oxopent-4-enoate ( [Kohler88, Kohler93] and in [Jaspers00]). The latter two reactions are shared with pathway dibenzofuran degradation. In addition, HbpA was also shown to hydroxylate 2,2',3-trihydroxybiphenyl to 2,2',3,3'-tetrahydroxybiphenyl, with subsequent metabolism via these enzymes to 2,3-dihydroxybenzoate, 2-oxopent-4-enoate, pyrogallol and (2E,4Z)-2-hydroxymuconate (2-hydroxymuconate), as shown here. However, the route via 2,2',3,3'-tetrahydroxybiphenyl was suggested to be a minor one [Kohler93].

Pathway 2-propylphenol degradation: A regulatory mutant of Pseudomonas nitroreducens, designated Prp, (Pseudomonas sp. strain HBP1 Prp, or Pseudomonas azelaica HBP1 Prp) was isolated by growth on 2-propylphenol. It was able to use this compound as a sole source of carbon and energy. 2-propylphenol did not support growth of wild-type Pseudomonas nitroreducens. The same enzymes that catalyze 2-hydroxybiphenyl degradation (HbpA, HbpC and HbpD) also appeared to catalyze 2-propylphenol degradation. The HbpA monooxygenase was induced by 2-propylphenol in the mutant, but not in the wild-type strain. In addition, a small amount of the first two enzymes were constitutively produced. Pathway intermediates of 2-propylphenol degradation were identified as 3-propylcatechol (the hydroxylation product), 2-hydroxy-6-oxo-nona-2,4-dienoate (the meta-cleavage product), and hydrolase products butanoate (butyrate) and 2-oxopent-4-enoate. However, it was noted that the pathway enzymes had higher affinities for the substrates of pathway 2-hydroxybiphenyl degradation [Kohler93a].

Pathway 2-isopropylphenol degradation: The Pseudomonas nitroreducens Prp regulatory mutant also utilized enzymes HbpA, HbpC and HbpD to degrade 2-isopropylphenol (o-cumenol) as the sole source of carbon and energy, with the corresponding intermediates 3-isopropylcatechol, 2-hydroxy-6-oxo-7-methyl-octa-2,4-dienoate, isobutanoate and 2-oxopent-4-enoate. 2-isopropylphenol is used in industry and is a potential pollutant [Reichlin94].

These pathways are an example of the generally broad specificity of enzymes functioning in meta-cleavage pathways [Kohler93a]. The Pseudomonas nitroreducens genes hbpA hbpC and hbpD encoding the three enzymes used in these pathways have been characterized. A regulatory gene hbpR was also identified and characterized as a member of the XylR/DmpR subclass of the NtrC family of transcriptional activators. Gene hbpR was shown to be necessary for transcriptional activation of these genes [Jaspers00, Jaspers01, Jaspers01a].

About This Pathway

The first reaction of this pathway is catalyzed by a Pseudomonas nitroreducens monooxygenase HbpA that has been designated as EC [Kohler88]. The second reaction is catalyzed by HbpB, a meta-cleaving dioxygenase. The third reaction is catalyzed by HbpC, a hydrolase that cleaves the meta-cleavage product to benzoate and 2-oxopent-4-enoate (which has an enol tautomeric form (2E)-2-hydroxypenta-2,4-dienoate) [Kohler88]. benzoate is further degraded by benzoate 1,2-dioxygenase to catechol, as shown in the pathway link. catechol is metabolized in the well characterized lower meta-cleavage pathway (see pathways catechol degradation I (meta-cleavage pathway) and catechol degradation II (meta-cleavage pathway)). 2-oxopent-4-enoate is degraded to acetyl-CoA which enters the TCA cycle I (prokaryotic), as shown in the pathway link (in [Jaspers00]).

Created 07-Mar-2012 by Fulcher CA, SRI International


Jaspers00: Jaspers MC, Suske WA, Schmid A, Goslings DA, Kohler HP, van der Meer JR (2000). "HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1." J Bacteriol 182(2);405-17. PMID: 10629187

Jaspers01: Jaspers MC, Schmid A, Sturme MH, Goslings DA, Kohler HP, Roelof Van Der Meer J (2001). "Transcriptional organization and dynamic expression of the hbpCAD genes, which encode the first three enzymes for 2-hydroxybiphenyl degradation in Pseudomonas azelaica HBP1." J Bacteriol 183(1);270-9. PMID: 11114926

Jaspers01a: Jaspers MC, Sturme M, van der Meer JR (2001). "Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of "Pseudomonas azelaica" HBP1." Microbiology 147(Pt 8);2183-94. PMID: 11495995

Kohler88: Kohler HP, Kohler-Staub D, Focht DD (1988). "Degradation of 2-hydroxybiphenyl and 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1." Appl Environ Microbiol 54(11);2683-8. PMID: 3214154

Kohler93: Kohler HP, Schmid A, van der Maarel M (1993). "Metabolism of 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1: production and consumption of 2,2',3-trihydroxybiphenyl." J Bacteriol 175(6);1621-8. PMID: 8449871

Kohler93a: Kohler HP, van der Maarel MJ, Kohler-Staub D (1993). "Selection of Pseudomonas sp. strain HBP1 Prp for metabolism of 2-propylphenol and elucidation of the degradative pathway." Appl Environ Microbiol 59(3);860-6. PMID: 8481010

Reichlin94: Reichlin F, Kohler HP (1994). "Pseudomonas sp. strain HBP1 Prp degrades 2-isopropylphenol (ortho-cumenol) via meta cleavage." Appl Environ Microbiol 60(12);4587-91. PMID: 7811094

Suske97: Suske WA, Held M, Schmid A, Fleischmann T, Wubbolts MG, Kohler HP (1997). "Purification and characterization of 2-hydroxybiphenyl 3-monooxygenase, a novel NADH-dependent, FAD-containing aromatic hydroxylase from Pseudomonas azelaica HBP1." J Biol Chem 272(39);24257-65. PMID: 9305879

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Goncalves06: Goncalves ER, Hara H, Miyazawa D, Davies JE, Eltis LD, Mohn WW (2006). "Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp. strain RHA1." Appl Environ Microbiol 72(9);6183-93. PMID: 16957245

He99: He Z, Spain JC (1999). "Comparison of the downstream pathways for degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45 (2-aminophenol pathway) and by Comamonas sp. JS765 (catechol pathway)." Arch Microbiol 171(5);309-16. PMID: 10382261

Held99: Held M, Schmid A, Kohler HP, Suske W, Witholt B, Wubbolts MG (1999). "An integrated process for the production of toxic catechols from toxic phenols based on a designer biocatalyst." Biotechnol Bioeng 62(6);641-8. PMID: 9951522

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Masai95: Masai E, Yamada A, Healy JM, Hatta T, Kimbara K, Fukuda M, Yano K (1995). "Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1." Appl Environ Microbiol 61(6);2079-85. PMID: 7793929

Meyer02: Meyer A, Wursten M, Schmid A, Kohler HP, Witholt B (2002). "Hydroxylation of indole by laboratory-evolved 2-hydroxybiphenyl 3-monooxygenase." J Biol Chem 277(37);34161-7. PMID: 12105208

Meyer02a: Meyer A, Schmid A, Held M, Westphal AH, Rothlisberger M, Kohler HP, van Berkel WJ, Witholt B (2002). "Changing the substrate reactivity of 2-hydroxybiphenyl 3-monooxygenase from Pseudomonas azelaica HBP1 by directed evolution." J Biol Chem 277(7);5575-82. PMID: 11733527

Meyer03: Meyer A, Tanner D, Schmid A, Sargent DF, Kohler HP, Witholt B (2003). "Crystallization and preliminary X-ray analysis of native and selenomethionine 2-hydroxybiphenyl 3-monooxygenase." Acta Crystallogr D Biol Crystallogr 59(Pt 4);741-3. PMID: 12657798

Meyer03a: Meyer A, Held M, Schmid A, Kohler HP, Witholt B (2003). "Synthesis of 3-tert-butylcatechol by an engineered monooxygenase." Biotechnol Bioeng 81(5);518-24. PMID: 12514800

Omori86: Omori, T., Sugimura, K., Ishigooka, H., Minoda, Y. (1986). "Purification and some properties of a 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolyzing enzyme from Pseudomonas cruciviae S93 B1 involved in the degradation of biphenyl." Agric. Biol. Chem. 50: 931-937.

Suske99: Suske WA, van Berkel WJ, Kohler HP (1999). "Catalytic mechanism of 2-hydroxybiphenyl 3-monooxygenase, a flavoprotein from Pseudomonas azelaica HBP1." J Biol Chem 274(47);33355-65. PMID: 10559214

Yamada98a: Yamada A, Kishi H, Sugiyama K, Hatta T, Nakamura K, Masai E, Fukuda M (1998). "Two nearly identical aromatic compound hydrolase genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1." Appl Environ Microbiol 64(6);2006-12. PMID: 9603807

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Mon May 2, 2016, biocyc14.