MetaCyc Pathway: 4-nitrophenol degradation II
Inferred from experiment

Enzyme View:

Pathway diagram: 4-nitrophenol degradation II

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.

Synonyms: p-nitrophenol degradation II

Superclasses: Degradation/Utilization/AssimilationAromatic Compounds DegradationNitroaromatic Compounds DegradationNitrophenol Degradation4-Nitrophenol Degradation
Degradation/Utilization/AssimilationAromatic Compounds DegradationPhenolic Compounds DegradationNitrophenol Degradation4-Nitrophenol Degradation

Some taxa known to possess this pathway include : Arthrobacter sp., Lysinibacillus sphaericus, Pseudomonas sp. 1-7, Rhodococcus opacus, Rhodococcus opacus SAO101 [Kitagawa04], Rhodococcus sp. PN1, Serratia sp. DS001, Sphingobium chlorophenolicum, Sphingomonas sp. UG30

Expected Taxonomic Range: Bacteria

General Background

The main input of 4-nitrophenol (p-nitrophenol, PNP) into the environment is the hydrolysis of methyl parathion or parathion, which are commonly used as pesticides in agriculture (see parathion degradation). PNP is also found in industrial wastes since it is a precursor not only of of pesticides such as carbofuran, nitrofen, methyl parathion and parathion, but also of certain pharmaceuticals, plasticizers, azo dyes, explosives etc. In addition, diesel fuel and gasoline exhaust also contain PNP [Tremp93]. Because of the widespread nature of p-nitrophenol and other nitrophenols, they are considered as major pollutants by the United States Environmental Protection Agency (USEPA).

Several bacterial species have the ability to degrade 4-nitrophenol. These include Nocardia [Hanne93], Arthrobacter [Jain94], Sphingobium chlorophenolicum and Sphingomonas sp. UG30 [Leung97], Flavobacterium [Raymond71], Burkholderia cepacia [Prakash96], Lysinibacillus sphaericus [Kadiyala98], Rhodococcus opacus SAO101 [Kitagawa04], Pseudomonas [Munnecke76] and Moraxella [Spain91]. In general, aerobic degradation of PNP by Gram-negative bacteria is initiated by formation of 1,4-benzoquinone (see 4-nitrophenol degradation I), while the first intermediate of PNP degradation by Gram-positive bacteria is 4-nitrocatechol (this pathway). Exceptions, however, do occur. For example, Serratia sp. DS001 is a Gram-negative organism that degrades PNP via 4-nitrocatechol [Pakala07], and the Gram-negative bacterium Pseudomonas sp. 1-7 possesses both pathways [Zhang12a].

About This Pathway

The key enzyme in this 4-nitrophenol degradation pathway is a two-component hydroxylase that oxidizes PNP to 4-nitrocatechol. The hydroxylase has been detected in several organisms, both Gram-positive and Gram-negative, including Nocardia [Mitra84], Lysinibacillus sphaericus JS905 [Kadiyala98], Rhodococcus sp. PN1 [Takeo03], Rhodococcus opacus SAO101 [Kitagawa04] and Serratia sp. DS001 [Pakala07].

Memebers of this family include two components: an oxygenase, which catalyzes the oxidation of the substrates using reduced flavins, and a reductase whose role is the replenishing of the reduced flavins. A single enzyme from this family catalyzes the first two steps of this pathway [Kadiyala98, Takeo03]. The enzyme generates hydroxyquinol and releases stoichiometric amounts of nitrite. hydroxyquinol is then oxidized to 2-maleylacetate, which is converted to 3-oxoadipate and shuttled through the 3-oxoadipate degradation pathway to central metabolism.

Variants: 4-nitrophenol degradation I

Relationship Links: Eawag-BBD-Pathways:PART-OF:nphe

Created 23-Feb-2007 by Caspi R, SRI International


Hanne93: Hanne LF, Kirk LL, Appel SM, Narayan AD, Bains KK (1993). "Degradation and induction specificity in actinomycetes that degrade p-nitrophenol." Appl Environ Microbiol 59(10);3505-8. PMID: 8250573

Jain94: Jain RK, Dreisbach JH, Spain JC (1994). "Biodegradation of p-nitrophenol via 1,2,4-benzenetriol by an Arthrobacter sp." Appl Environ Microbiol 60(8);3030-2. PMID: 8085840

Kadiyala98: Kadiyala V, Spain JC (1998). "A two-component monooxygenase catalyzes both the hydroxylation of p-nitrophenol and the oxidative release of nitrite from 4-nitrocatechol in Bacillus sphaericus JS905." Appl Environ Microbiol 64(7);2479-84. PMID: 9647818

Kitagawa04: Kitagawa W, Kimura N, Kamagata Y (2004). "A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101." J Bacteriol 186(15);4894-902. PMID: 15262926

Leung97: Leung, K.T., Tresse, O., Errampalli, D., Lee, H., Trevors, J.T. (1997). "Mineralization of p-nitrophenol by pentachlorophenol-degrading Sphingomonas spp." FEMS Microbiol. Lett. 155: 107-114.

Mitra84: Mitra D, Vaidyanathan CS (1984). "A new 4-nitrophenol 2-hydroxylase from a Nocardia sp." Biochem Int 8(5);609-15. PMID: 6477623

Munnecke76: Munnecke DM, Hsieh DP (1976). "Pathways of microbial metabolism of parathion." Appl Environ Microbiol 1976;31(1);63-9. PMID: 8005

Pakala07: Pakala SB, Gorla P, Pinjari AB, Krovidi RK, Baru R, Yanamandra M, Merrick M, Siddavattam D (2007). "Biodegradation of methyl parathion and p-nitrophenol: evidence for the presence of a p-nitrophenol 2-hydroxylase in a Gram-negative Serratia sp. strain DS001." Appl Microbiol Biotechnol 73(6);1452-62. PMID: 17043828

Prakash96: Prakash D, Chauhan A, Jain RK (1996). "Plasmid-encoded degradation of p-nitrophenol by Pseudomonas cepacia." Biochem Biophys Res Commun 224(2);375-81. PMID: 8702398

Raymond71: Raymond, D.G.M., Alexander, M. (1971). "Microbial metabolism and cometabolism of nitrophenols." Pestic. Biochem. Physiol. 1: 123-130.

Spain91: Spain JC, Gibson DT (1991). "Pathway for Biodegradation of p-Nitrophenol in a Moraxella sp." Appl Environ Microbiol 57(3);812-819. PMID: 16348446

Takeo03: Takeo M, Yasukawa T, Abe Y, Niihara S, Maeda Y, Negoro S (2003). "Cloning and characterization of a 4-nitrophenol hydroxylase gene cluster from Rhodococcus sp. PN1." J Biosci Bioeng 95(2);139-45. PMID: 16233382

Tremp93: Tremp, J., Mattrel, P, Fingler, S., Giger, W. (1993). "Phenols and nitrophenols as tropospheric pollutants: emissions from automobile exhausts and phase transfer in the atmosphere." Water Air Soil Poll. 68: 113-123.

Zhang12a: Zhang S, Sun W, Xu L, Zheng X, Chu X, Tian J, Wu N, Fan Y (2012). "Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in pseudomonas sp. 1-7." BMC Microbiol 12;27. PMID: 22380602

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

Bondarenko04: Bondarenko S, Gan J, Haver DL, Kabashima JN (2004). "Persistence of selected organophosphate and carbamate insecticides in waters from a coastal watershed." Environ Toxicol Chem 23(11);2649-54. PMID: 15559280

Cai02: Cai M, Xun L (2002). "Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723." J Bacteriol 184(17);4672-80. PMID: 12169590

Daubaras96: Daubaras DL, Saido K, Chakrabarty AM (1996). "Purification of hydroxyquinol 1,2-dioxygenase and maleylacetate reductase: the lower pathway of 2,4,5-trichlorophenoxyacetic acid metabolism by Burkholderia cepacia AC1100." Appl Environ Microbiol 62(11);4276-9. PMID: 8900023

Endo05: Endo R, Kamakura M, Miyauchi K, Fukuda M, Ohtsubo Y, Tsuda M, Nagata Y (2005). "Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26." J Bacteriol 187(3);847-53. PMID: 15659662

Halak07: Halak S, Basta T, Burger S, Contzen M, Wray V, Pieper DH, Stolz A (2007). "4-sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2." J Bacteriol 189(19);6998-7006. PMID: 17660282

Huang06: Huang Y, Zhao KX, Shen XH, Chaudhry MT, Jiang CY, Liu SJ (2006). "Genetic characterization of the resorcinol catabolic pathway in Corynebacterium glutamicum." Appl Environ Microbiol 72(11);7238-45. PMID: 16963551

Kasai15: Kasai D, Araki N, Motoi K, Yoshikawa S, Iino T, Imai S, Masai E, Fukuda M (2015). "γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1." Appl Environ Microbiol 81(21);7656-65. PMID: 26319878

Kasberg95: Kasberg T, Daubaras DL, Chakrabarty AM, Kinzelt D, Reineke W (1995). "Evidence that operons tcb, tfd, and clc encode maleylacetate reductase, the fourth enzyme of the modified ortho pathway." J Bacteriol 177(13);3885-9. PMID: 7601858

Kasberg97: Kasberg T, Seibert V, Schlomann M, Reineke W (1997). "Cloning, characterization, and sequence analysis of the clcE gene encoding the maleylacetate reductase of Pseudomonas sp. strain B13." J Bacteriol 179(11);3801-3. PMID: 9171435

Kaschabek92: Kaschabek SR, Reineke W (1992). "Maleylacetate reductase of Pseudomonas sp. strain B13: dechlorination of chloromaleylacetates, metabolites in the degradation of chloroaromatic compounds." Arch Microbiol 158(6);412-7. PMID: 1482270

Kaschabek93: Kaschabek SR, Reineke W (1993). "Degradation of chloroaromatics: purification and characterization of maleylacetate reductase from Pseudomonas sp. strain B13." J Bacteriol 175(19);6075-81. PMID: 8407778

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

Mattozzi10: Mattozzi Mde L, Keasling JD (2010). "Rationally engineered biotransformation of p-nitrophenol." Biotechnol Prog 26(3);616-21. PMID: 20196144

Matus03: Matus V, Sanchez MA, Martinez M, Gonzalez B (2003). "Efficient degradation of 2,4,6-Trichlorophenol requires a set of catabolic genes related to tcp genes from Ralstonia eutropha JMP134(pJP4)." Appl Environ Microbiol 69(12);7108-15. PMID: 14660355

Nikodem03: Nikodem P, Hecht V, Schlomann M, Pieper DH (2003). "New bacterial pathway for 4- and 5-chlorosalicylate degradation via 4-chlorocatechol and maleylacetate in Pseudomonas sp. strain MT1." J Bacteriol 185(23);6790-800. PMID: 14617643

Perry07: Perry LL, Zylstra GJ (2007). "Cloning of a gene cluster involved in the catabolism of p-nitrophenol by Arthrobacter sp. strain JS443 and characterization of the p-nitrophenol monooxygenase." J Bacteriol 189(21);7563-72. PMID: 17720792

Seibert93: Seibert V, Stadler-Fritzsche K, Schlomann M (1993). "Purification and characterization of maleylacetate reductase from Alcaligenes eutrophus JMP134(pJP4)." J Bacteriol 175(21);6745-54. PMID: 8226615

Seibert98: Seibert V, Kourbatova EM, Golovleva LA, Schlomann M (1998). "Characterization of the maleylacetate reductase MacA of Rhodococcus opacus 1CP and evidence for the presence of an isofunctional enzyme." J Bacteriol 180(14);3503-8. PMID: 9657989

Shen05: Shen XH, Huang Y, Liu SJ (2005). "Genomic Analysis and Identification of Catabolic Pathways for Aromatic Compounds in Corynebacterium glutamicum." Microbes and Environments 20(3);160-167.

Shen10: Shen W, Liu W, Zhang J, Tao J, Deng H, Cao H, Cui Z (2010). "Cloning and characterization of a gene cluster involved in the catabolism of p-nitrophenol from Pseudomonas putida DLL-E4." Bioresour Technol 101(19);7516-22. PMID: 20466541

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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
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