Note: a dashed line (without arrowheads) between two compound names is meant to imply that the two names are just different instantiations of the same compound -- i.e. one may be a specific name and the other a general name, or they may both represent the same compound in different stages of a polymerization-type pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
|Superclasses:||Degradation/Utilization/Assimilation → Aromatic Compounds Degradation|
Expected Taxonomic Range: Bacteria
Lignin is the most abundant aromatic compound in nature, and its mineralization is an important step in the terrestrial carbon cycle. Lignin is broken down to various biaryl and monoaryl compounds such as biphenyl, ferulate, vanillate and syringate.
Complex lignin is resistant to bacterial enzymes. Its degradation is initiated by white rot fungi, which secrete extracellular degradation enzymes such as lignin peroxidase, manganese peroxidase, and laccase [Gold93]. The resulting low-molecular-weight lignin can be further degraded and mineralized by bacteria [Ruttimann91].
Sphingomonas sp. SYK6 is able to grow on many of these compounds as the sole sources of carbon and energy. It degrades lignin-derived compounds possessing guaiacyl (4-hydroxy-3-methoxyphenyl) and syringyl (4-hydroxy-3,5-dimethoxyphenyl) moieties to vanillate and syringate, respectively, and is able to completely mineralize these two compounds as described in the superpathway of vanillin and vanillate degradation and syringate degradation pathways.
About This Pathway
Syringate degradation begins with its conversion to 3-O-methylgallate by the tetrahydrofolate-dependent syringate O-demethylase (encoded by desA) [Masai04]. 3-O-methylgallate can be degraded further via three different routes that converge back at (1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate.
The main route, via gallate , is catalyzed by two enzymes - a second tetrahydrofolate-dependent demethylase, vanillate/3-O-methylgallate O-demethylase (ligM), and gallate dioxygenase (desB) [Kasai05].
The other two routes are the result of direct dioxygenation of 3-O-methylgallate. This reaction is carried out by two dioxygenases - protocatechuate 4,5-dioxygenase (ligA and ligB) and 3-O-methylgallate 3,4-dioxygenase (desZ), both of which produce a mixture of two different products - 2-pyrone-4,6-dicarboxylate (PDC) and 5-carboxyvanillate (CHMOD) [Kasai07]. The first product is hydrolized by 2-pyrone-4,6-dicarboxylate hydrolase (ligI). The second product is converted to (1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate in a route that hasn't been characterized yet.
(1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate spontaneously converts to its tautomeric form (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate, which is degraded into TCA cycle intermediates by the action of two additional enzymes - 4-oxalomesaconate hydratase (ligJ) and oxaloacetate β-decarboxylase / 4-oxalocitramalate aldolase (ligK).
Subpathways: gallate degradation I
Kasai05: Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2005). "Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6." J Bacteriol 187(15);5067-74. PMID: 16030198
Kasai07: Kasai D, Masai E, Katayama Y, Fukuda M (2007). "Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase." FEMS Microbiol Lett 274(2);323-8. PMID: 17645527
Masai04: Masai E, Sasaki M, Minakawa Y, Abe T, Sonoki T, Miyauchi K, Katayama Y, Fukuda M (2004). "A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate." J Bacteriol 186(9);2757-65. PMID: 15090517
Nishikawa98: Nishikawa S, Sonoki T, Kasahara T, Obi T, Kubota S, Kawai S, Morohoshi N, Katayama Y (1998). "Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate." Appl Environ Microbiol 64(3);836-42. PMID: 9501423
Ruttimann91: Ruttimann C, Vicuna R, Mozuch MD, Kirk TK (1991). "Limited bacterial mineralization of fungal degradation intermediates from synthetic lignin." Appl Environ Microbiol 57(12);3652-5. PMID: 1785937
Abe05: Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M (2005). "A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6." J Bacteriol 187(6);2030-7. PMID: 15743951
Hara00: Hara H, Masai E, Katayama Y, Fukuda M (2000). "The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6." J Bacteriol 182(24);6950-7. PMID: 11092855
Hara03: Hara H, Masai E, Miyauchi K, Katayama Y, Fukuda M (2003). "Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6." J Bacteriol 185(1);41-50. PMID: 12486039
Kasai04: Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2004). "Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6." J Bacteriol 186(15);4951-9. PMID: 15262932
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Maruyama01: Maruyama K, Miwa M, Tsujii N, Nagai T, Tomita N, Harada T, Sobajima H, Sugisaki H (2001). "Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1." Biosci Biotechnol Biochem 65(12);2701-9. PMID: 11826967
Maruyama90: Maruyama K (1990). "Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae grown on phthalate." J Biochem (Tokyo) 1990;108(2);327-33. PMID: 2229032
Masai00: Masai E, Momose K, Hara H, Nishikawa S, Katayama Y, Fukuda M (2000). "Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6." J Bacteriol 182(23);6651-8. PMID: 11073908
Masai02: Masai E, Harada K, Peng X, Kitayama H, Katayama Y, Fukuda M (2002). "Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6." Appl Environ Microbiol 68(9);4416-24. PMID: 12200295
Masai99: Masai E, Shinohara S, Hara H, Nishikawa S, Katayama Y, Fukuda M (1999). "Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6." J Bacteriol 181(1);55-62. PMID: 9864312
Noda90: Noda Y, Nishikawa S, Shiozuka K, Kadokura H, Nakajima H, Yoda K, Katayama Y, Morohoshi N, Haraguchi T, Yamasaki M (1990). "Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis." J Bacteriol 172(5);2704-9. PMID: 2185230
Nogales05: Nogales J, Canales A, Jimenez-Barbero J, Garcia JL, Diaz E (2005). "Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440: The prototype of a new subgroup of extradiol dioxygenases." J Biol Chem 280(42):35382-90. PMID: 16030014
Nogales10: Nogales, J., Canales, A., Jimenez-barbero, J., Serra, B., Pingarron, J. M., Garcia, J. L., Diaz, E. (2010). "Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida." Molecular Microbiology, 79:359-374. PMID: 21219457
Nogales11: Nogales J, Canales A, Jimenez-Barbero J, Serra B, Pingarron JM, Garcia JL, Diaz E (2011). "Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida." Mol Microbiol 79(2);359-74. PMID: 21219457
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