Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| cis-calamenene related sesquiterpenoids biosynthesis Accession ID: BioCyc:META_PWY-6128 |
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Prosser IM, Adams RJ, Beale MH, Hawkins ND, Phillips AL, Pickett JA, Field LM. Cloning and functional characterisation of a cis-muuroladiene synthase from black peppermint (Mentha×piperita) and direct evidence for a chemotype unable to synthesise farnesene. Phytochemistry. 2006 Aug;67(15):1564–71. doi: 10.1016/j.phytochem.2005.06.012. |
| assimilatory sulfate reduction II Accession ID: BioCyc:META_SULFMETII-PWY |
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Kopriva S, Koprivova A. Plant adenosine 5'-phosphosulphate reductase: the past, the present, and the future. J Exp Bot. 2004 Aug;55(404):1775–83. doi: 10.1093/jxb/erh185. PMID: 15208336.; Neumann S, Wynen A, Trüper HG, Dahl C. Characterization of the cys gene locus from Allochromatium vinosum indicates an unusual sulfate assimilation pathway. Mol Biol Rep. 2000 Mar;27(1):27–33. doi: 10.1023/a:1007058421714. PMID: 10939523. |
| mannojirimycin biosynthesis Accession ID: BioCyc:META_PWY-7531 |
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Wu Y, Arciola J, Horenstein N. Medium-chain dehydrogenases with new specificity: amino mannitol dehydrogenases on the azasugar biosynthetic pathway. Protein Pept Lett. 2014;21(1):10–4. doi: 10.2174/092986652101131219093413. PMID: 24354768.; Clark LF, Johnson JV, Horenstein NA. Identification of a gene cluster that initiates azasugar biosynthesis in Bacillus amyloliquefaciens. Chembiochem. 2011 Sep 19;12(14):2147–50. doi: 10.1002/cbic.201100347. PMID: 21786380.; Kang KD, Cho YS, Song JH, Park YS, Lee JY, Hwang KY, Rhee SK, Chung JH, Kwon O, Seong SI. Identification of the genes involved in 1-deoxynojirimycin synthesis in Bacillus subtilis MORI 3K-85. J Microbiol. 2011 Jun;49(3):431–40. doi: 10.1007/s12275-011-1238-3. PMID: 21717329. |
| germacrene biosynthesis Accession ID: BioCyc:META_PWY-5733 |
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Picaud S, Olsson ME, Brodelius M, Brodelius PE. Cloning, expression, purification and characterization of recombinant (+)-germacrene D synthase from Zingiber officinale. Archives of Biochemistry and Biophysics. 2006 Aug;452(1):17–28. doi: 10.1016/j.abb.2006.06.007.; Steele CL, Crock J, Bohlmann J, Croteau R. Sesquiterpene synthases from grand fir (Abies grandis). Comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of delta-selinene synthase and gamma-humulene synthase. J Biol Chem. 1998 Jan 23;273(4):2078–89. doi: 10.1074/jbc.273.4.2078. PMID: 9442047. |
| (R)-cysteate degradation Accession ID: BioCyc:META_PWY-6642 |
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Rein U, Gueta R, Denger K, Ruff J, Hollemeyer K, Cook AM. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology (Reading). 2005 Mar;151(Pt 3):737–47. doi: 10.1099/mic.0.27548-0. PMID: 15758220.; Graupner M, White RH. The first examples of (S)-2-hydroxyacid dehydrogenases catalyzing the transfer of the pro-4S hydrogen of NADH are found in the archaea. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 2001 Jul;1548(1):169–73. doi: 10.1016/s0167-4838(01)00220-5.; Graupner M, Xu H, White RH. Identification of an Archaeal 2-Hydroxy Acid Dehydrogenase Catalyzing Reactions Involved in Coenzyme Biosynthesis in Methanoarchaea. J Bacteriol. 2000 Jul;182(13):3688–92. doi: 10.1128/jb.182.13.3688-3692.2000. |
| diacylglyceryl-N,N,N-trimethylhomoserine biosynthesis Accession ID: BioCyc:META_PWY-6795 |
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Riekhof WR, Andre C, Benning C. Two enzymes, BtaA and BtaB, are sufficient for betaine lipid biosynthesis in bacteria. Archives of Biochemistry and Biophysics. 2005 Sep;441(1):96–105. doi: 10.1016/j.abb.2005.07.001.; Klug RM, Benning C. Two enzymes of diacylglyceryl- O -4'-( N,N,N, -trimethyl)homoserine biosynthesis are encoded by btaA and btaB in the purple bacterium Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. U.S.A. 2001 May;98(10):5910–5. doi: 10.1073/pnas.101037998.; Janero DR, Barrnett R. Isolation and characterization of an ether-linked homoserine lipid from the thylakoid membrane of Chlamydomonas reinhardtii 137+. Journal of Lipid Research. 1982 Feb;23(2):307–16. doi: 10.1016/s0022-2275(20)38161-x. |
| sesquiterpenoid phytoalexins biosynthesis Accession ID: BioCyc:META_PWY-2961 |
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Takahashi S, Yeo Y, Zhao Y, O'Maille PE, Greenhagen BT, Noel JP, Coates RM, Chappell J. Functional Characterization of Premnaspirodiene Oxygenase, a Cytochrome P450 Catalyzing Regio- and Stereo-specific Hydroxylations of Diverse Sesquiterpene Substrates. Journal of Biological Chemistry. 2007 Oct;282(43):31744–54. doi: 10.1074/jbc.m703378200. |
| baicalein degradation (hydrogen peroxide detoxification) Accession ID: BioCyc:META_PWY-7214 |
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Gill SS, Tuteja N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem. 2010 Dec;48(12):909–30. doi: 10.1016/j.plaphy.2010.08.016. PMID: 20870416.; Sasaki K, Taura F, Shoyama Y, Morimoto S. Molecular Characterization of a Novel ß-Glucuronidase fromScutellaria baicalensis Georgi. Journal of Biological Chemistry. 2000 Sep;275(35):27466–72. doi: 10.1016/s0021-9258(19)61531-0.; Morimoto S, Tateishi N, Inuyama M, Taura F, Tanaka H, Shoyama Y. Identification and Molecular Characterization of Novel Peroxidase with Structural Protein-like Properties. Journal of Biological Chemistry. 1999 Sep;274(37):26192–8. doi: 10.1074/jbc.274.37.26192.; Morimoto S, Tateishi N, Matsuda T, Tanaka H, Taura F, Furuya N, Matsuyama N, Shoyama Y. Novel Hydrogen Peroxide Metabolism in Suspension Cells ofScutellaria baicalensis Georgi. Journal of Biological Chemistry. 1998 May;273(20):12606–11. doi: 10.1074/jbc.273.20.12606.; IKEGAMI F, MATSUNAE K, HISAMITSU M, KURIHARA T, YAMAMOTO T, MURAKOSHI I. Purification and Properties of a Plant .BETA.-D-Glucuronidase from Scutellaria Root. Biological & Pharmaceutical Bulletin. 1995;18(11):1531–4. doi: 10.1248/bpb.18.1531.; Mehdy MC. Active Oxygen Species in Plant Defense against Pathogens. Plant Physiol. 1994 Jun;105(2):467–72. PMID: 12232215; PMCID: PMC159383.; Vitorica J, Park D, Chin G, de Bias AL. Characterization with Antibodies of the ?-Aminobutyric AcidA/Benzodiazepine Receptor Complex During Development of the Rat Brain. Journal of Neurochemistry. 1990 Jan;54(1):187–94. doi: 10.1111/j.1471-4159.1990.tb13300.x. |
| superpathway of sulfate assimilation and cysteine biosynthesis Accession ID: BioCyc:META_SULFATE-CYS-PWY |
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| 3,3'-thiodipropanoate degradation Accession ID: BioCyc:META_PWY-7465 |
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Schürmann M, Deters A, Wübbeler JH, Steinbüchel A. A Novel 3-Sulfinopropionyl Coenzyme A (3SP-CoA) Desulfinase from Advenella mimigardefordensis Strain DPN7 T Acting as a Key Enzyme during Catabolism of 3,3'-Dithiodipropionic Acid Is a Member of the Acyl-CoA Dehydrogenase Superfamily. J Bacteriol. 2013 Apr;195(7):1538–51. doi: 10.1128/jb.02105-12.; Bruland N, Wu¨bbeler JH, Steinbu¨chel A. 3-Mercaptopropionate Dioxygenase, a Cysteine Dioxygenase Homologue, Catalyzes the Initial Step of 3-Mercaptopropionate Catabolism in the 3,3-Thiodipropionic Acid-degrading Bacterium Variovorax paradoxus. Journal of Biological Chemistry. 2009 Jan;284(1):660–72. doi: 10.1074/jbc.m806762200. |
| isethionate degradation Accession ID: BioCyc:META_PWY-2601 |
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Kondo H, Niki H, Takahashi S, Ishimoto M. Enzymatic oxidation of isethionate to sulfoacetaldehyde in bacterial extract. J Biochem. 1977 Jun;81(6):1911–6. doi: 10.1093/oxfordjournals.jbchem.a131653. PMID: 197072. |
| sulfur volatiles biosynthesis Accession ID: BioCyc:META_PWY-6736 |
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Attieh J, Djiana R, Koonjul P, Etienne C, Sparace SA, Saini HS. Cloning and functional expression of two plant thiol methyltransferases: a new class of enzymes involved in the biosynthesis of sulfur volatiles. Plant Mol Biol. 2002 Oct;50(3):511–21. doi: 10.1023/a:1019865829534. PMID: 12369626. |
| sulfoacetate degradation Accession ID: BioCyc:META_PWY-6593 |
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Weinitschke S, Hollemeyer K, Kusian B, Bowien B, Smits THM, Cook AM. Sulfoacetate Is Degraded via a Novel Pathway Involving Sulfoacetyl-CoA and Sulfoacetaldehyde in Cupriavidus necator H16. Journal of Biological Chemistry. 2010 Nov;285(46):35249–54. doi: 10.1074/jbc.m110.127043. |
| dimethyl sulfone degradation Accession ID: BioCyc:META_PWY-6058 |
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Borodina E, Kelly DP, Schumann P, Rainey FA, Ward-Rainey NL, Wood AP. Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Arch Microbiol. 2002 Feb;177(2):173–83. doi: 10.1007/s00203-001-0373-3. PMID: 11807567.; Borodina E, Kelly DP, Rainey FA, Ward-Rainey NL, Wood AP. Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter. Arch Microbiol. 2000 May;173(5-6):425–37. doi: 10.1007/s002030000165. PMID: 10896224. |
| ethanedisulfonate degradation Accession ID: BioCyc:META_PWY-6043 |
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Denger K, Cook AM. Ethanedisulfonate is degraded via sulfoacetaldehyde in Ralstonia sp. strain EDS1. Arch Microbiol. 2001 Jul;176(1-2):89–95. doi: 10.1007/s002030100296. PMID: 11479707. |
| dimethyl sulfide biosynthesis from methionine Accession ID: BioCyc:META_PWY-7793 |
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Carrión O, Curson ARJ, Kumaresan D, Fu Y, Lang AS, Mercadé E, Todd JD. A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments. Nat Commun. 2015 Mar 25;6():6579. doi: 10.1038/ncomms7579. PMID: 25807229. |
| methanogenesis from dimethylsulfide Accession ID: BioCyc:META_PWY-5258 |
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Tallant TC, Paul L, Krzycki JA. The MtsA Subunit of the Methylthiol:Coenzyme M Methyltransferase of Methanosarcina barkeri Catalyses Both Half-reactions of Corrinoid-dependent Dimethylsulfide: Coenzyme M Methyl Transfer. Journal of Biological Chemistry. 2001 Feb;276(6):4485–93. doi: 10.1074/jbc.m007514200. |
| 3-sulfopropanediol degradation Accession ID: BioCyc:META_PWY-6634 |
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Mayer J, Huhn T, Habeck M, Denger K, Hollemeyer K, Cook AM. 2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase. Microbiology (Reading). 2010 May;156(Pt 5):1556–64. doi: 10.1099/mic.0.037580-0. PMID: 20150239. |
| curcumene biosynthesis Accession ID: BioCyc:META_PWY-6257 |
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Deguerry F, Pastore L, Wu S, Clark A, Chappell J, Schalk M. The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Archives of Biochemistry and Biophysics. 2006 Oct;454(2):123–36. doi: 10.1016/j.abb.2006.08.006. |
| 4,4'-disulfanediyldibutanoate degradation Accession ID: BioCyc:META_PWY-7898 |
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Wübbeler JH, Bruland N, Wozniczka M, Steinbüchel A. Biodegradation of the xenobiotic organic disulphide 4,4'-dithiodibutyric acid by Rhodococcus erythropolis strain MI2 and comparison with the microbial utilization of 3,3'-dithiodipropionic acid and 3,3'-thiodipropionic acid. Microbiology (Reading). 2010 Apr;156(Pt 4):1221–33. doi: 10.1099/mic.0.036178-0. PMID: 19959574. |