Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store

MetaCyc Pathway: naphthalene degradation (aerobic)
Inferred from experiment

Enzyme View:

Pathway diagram: naphthalene degradation (aerobic)

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 DegradationNaphthalene Degradation

Some taxa known to possess this pathway include : Pseudomonas putida ATCC 17484, pseudomonas putida NP, Pseudomonas putida PpG7, Pseudomonas sp. ATCC 17483, Pseudomonas sp. NCIB9816-4, Pseudomonas sp. PG, Pseudomonas stutzeri AN10, Ralstonia sp. U2, Rhodococcus sp. NCIMB12038

Expected Taxonomic Range: Bacteria

Naphthalene is the simplest fused polycyclic aromatic hydrocarbon, and is abundant in soils. Several bacterial species are able to grow on naphthalene as the sole cource of carbon and energy [Shamsuzzaman74, Bosch99, Kulakov00]. At least two pathways for naphthalene degradation exist - an aerobic pathway and an anaerobic pathway. This pathway describes the aerobic process.

Naphthalene is catabolized through cis naphthalene dihydrodiol, salicylaldehyde, and salicylate. The latter is converted into either catechol, which is then degraded by either the meta or the ortho cleavage pathways to TCA cycle intermediates [Barnsley76], or to gentisate, which is degraded by a different pathway to TCA cycle intermediates [Fuenmayor98] (see salicylate degradation I and salicylate degradation II, respectively).

Several different models have been proposed for this pathway, due to the difficulty working with the unstable intermediate naphthalene-1,2-diol, which is rapidly and spontaneously oxidized in water to 1,2-naphthoquinone. The pathway presented here reflects the results of a careful analysis performed by Eaton and Chapman [Eaton92].

The genes encoding the enzymes required for the catabolism of naphthalene are often carried on plasmids, such as the NAH plasmids [Zakharian, Connors82, Yen82]. However, some organisms, such as Pseudomonas stutzeri AN10, carry these genes on their chromosome [Bosch99]. Transcription of the genes in this operon is regulated by a salicylate-dependent transcription regulator (such as NahR for the operon located on the NAH plasmid) [You86, Schell86].

Superpathways: naphthalene degradation to acetyl-CoA, superpathway of aromatic compound degradation via 2-oxopent-4-enoate

Variants: naphthalene degradation (anaerobic)

Unification Links: Eawag-BBD-Pathways:naph

Created 06-Dec-2006 by Caspi R, SRI International


Barnsley76: Barnsley EA (1976). "Role and regulation of the ortho and meta pathways of catechol metabolism in pseudomonads metabolizing naphthalene and salicylate." J Bacteriol 125(2);404-8. PMID: 1245462

Bosch99: Bosch R, Garcia-Valdes E, Moore ER (1999). "Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10." Gene 236(1);149-57. PMID: 10433976

Connors82: Connors MA, Barnsley EA (1982). "Naphthalene plasmids in pseudomonads." J Bacteriol 149(3);1096-101. PMID: 6277849

Eaton92: Eaton RW, Chapman PJ (1992). "Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions." J Bacteriol 174(23);7542-54. PMID: 1447127

Fuenmayor98: Fuenmayor SL, Wild M, Boyes AL, Williams PA (1998). "A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2." J Bacteriol 180(9);2522-30. PMID: 9573207

Kulakov00: Kulakov LA, Allen CC, Lipscomb DA, Larkin MJ (2000). "Cloning and characterization of a novel cis-naphthalene dihydrodiol dehydrogenase gene (narB) from Rhodococcus sp. NCIMB12038." FEMS Microbiol Lett 182(2);327-31. PMID: 10620687

Schell86: Schell MA, Wender PE (1986). "Identification of the nahR gene product and nucleotide sequences required for its activation of the sal operon." J Bacteriol 166(1);9-14. PMID: 3007442

Shamsuzzaman74: Shamsuzzaman KM, Barnsley EA (1974). "The regulation of naphthalene metabolism in pseudomonads." Biochem Biophys Res Commun 60(2);582-9. PMID: 4423716

Yen82: Yen KM, Gunsalus IC (1982). "Plasmid gene organization: naphthalene/salicylate oxidation." Proc Natl Acad Sci U S A 79(3);874-8. PMID: 6278499

You86: You IS, Gunsalus IC (1986). "Regulation of the nah and sal operons of plasmid NAH7: evidence for a new function in nahR." Biochem Biophys Res Commun 141(3);986-92. PMID: 3028396

Zakharian: Zakharian RA, Bakunin KA, Gasparian NS, Kocharian ShM, Arakelov GM "[Plasmid characteristics of naphthalene and salicylate biodegradation in Pseudomonas putida]." Mikrobiologiia 49(6);931-5. PMID: 6259498

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

Beil97: Beil S, Happe B, Timmis KN, Pieper DH (1997). "Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12--dechlorination of 1,2,4,5-tetrachlorobenzene." Eur J Biochem 247(1);190-9. PMID: 9249026

Boronin89: Boronin AM, Tsoi TV, Kosheleva IA, Arinbasarov MU, Adanin VM (1989). "[Cloning of Pseudomonas putida genes responsible for the primary stages of oxidation of naphthalene in Escherichia coli cells]." Genetika 25(2);226-37. PMID: 2661326

Dennis04: Dennis JJ, Zylstra GJ (2004). "Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4." J Mol Biol 341(3);753-68. PMID: 15288784

Eaton00: Eaton RW (2000). "trans-o-Hydroxybenzylidenepyruvate hydratase-aldolase as a biocatalyst." Appl Environ Microbiol 66(6);2668-72. PMID: 10831455

Ensley82: Ensley BD, Gibson DT, Laborde AL (1982). "Oxidation of naphthalene by a multicomponent enzyme system from Pseudomonas sp. strain NCIB 9816." J Bacteriol 149(3);948-54. PMID: 7037744

Ensley83: Ensley BD, Ratzkin BJ, Osslund TD, Simon MJ, Wackett LP, Gibson DT (1983). "Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo." Science 222(4620);167-9. PMID: 6353574

Ensley83a: Ensley BD, Gibson DT (1983). "Naphthalene dioxygenase: purification and properties of a terminal oxygenase component." J Bacteriol 155(2);505-11. PMID: 6874638

Ensley90: Ensley BD, Haigler BE (1990). "Naphthalene dioxygenase from Pseudomonas NCIB 9816." Methods Enzymol 188;46-52. PMID: 2280717

Gibson95: Gibson DT, Resnick SM, Lee K, Brand JM, Torok DS, Wackett LP, Schocken MJ, Haigler BE (1995). "Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4." J Bacteriol 177(10);2615-21. PMID: 7751268

Haigler90: Haigler BE, Gibson DT (1990). "Purification and properties of NADH-ferredoxinNAP reductase, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816." J Bacteriol 172(1);457-64. PMID: 2294092

Haigler90a: Haigler BE, Gibson DT (1990). "Purification and properties of ferredoxinNAP, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816." J Bacteriol 172(1);465-8. PMID: 2294093

Kauppi98: Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S (1998). "Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase." Structure 6(5);571-86. PMID: 9634695

Kurkela88: Kurkela S, Lehvaslaiho H, Palva ET, Teeri TH (1988). "Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816." Gene 73(2);355-62. PMID: 3243438

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

Lessner02: Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT (2002). "Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765." Appl Environ Microbiol 68(2);634-41. PMID: 11823201

Parales05: Parales RE, Huang R, Yu CL, Parales JV, Lee FK, Lessner DJ, Ivkovic-Jensen MM, Liu W, Friemann R, Ramaswamy S, Gibson DT (2005). "Purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems." Appl Environ Microbiol 71(7);3806-14. PMID: 16000792

Patel74: Patel TR, Gibson DT (1974). "Purification and propeties of (plus)-cis-naphthalene dihydrodiol dehydrogenase of Pseudomonas putida." J Bacteriol 119(3);879-88. PMID: 4369091

Patel80: Patel TR, Barnsley EA (1980). "Naphthalene metabolism by pseudomonads: purification and properties of 1,2-dihydroxynaphthalene oxygenase." J Bacteriol 143(2);668-73. PMID: 7204331

Resnick96: Resnick SM, Gibson DT (1996). "Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4." Appl Environ Microbiol 62(11);4073-80. PMID: 8899998

Schell83: Schell MA (1983). "Cloning and expression in Escherichia coli of the naphthalene degradation genes from plasmid NAH7." J Bacteriol 153(2);822-9. PMID: 6296054

Showing only 20 references. To show more, press the button "Show all references".

Report Errors or Provide Feedback
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 Sun Feb 7, 2016, biocyc11.