Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| styrene degradation Accession ID: BioCyc:META_PWY-6941 |
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Beltrametti F, Marconi AM, Bestetti G, Colombo C, Galli E, Ruzzi M, Zennaro E. Sequencing and functional analysis of styrene catabolism genes from Pseudomonas fluorescens ST. Appl Environ Microbiol. 1997 Jun;63(6):2232–9. doi: 10.1128/aem.63.6.2232-2239.1997.; Hartmans S, van der Werf MJ, de Bont JA. Bacterial degradation of styrene involving a novel flavin adenine dinucleotide-dependent styrene monooxygenase. Appl Environ Microbiol. 1990 May;56(5):1347–51. doi: 10.1128/aem.56.5.1347-1351.1990. |
| penicillin G and penicillin V biosynthesis Accession ID: BioCyc:META_PWY-7716 |
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Kistler HC, Broz K. Cellular compartmentalization of secondary metabolism. Front. Microbiol. 2015 Feb 09;6(). doi: 10.3389/fmicb.2015.00068.; Clement ME, Okeke NL, Hicks CB. Treatment of syphilis: a systematic review. JAMA. 2014 Nov 12;312(18):1905–17. PMID: 25387188; PMCID: PMC6690208.; Martín JF, García-Estrada C, Ullán RV. Transport of substrates into peroxisomes: the paradigm of ß-lactam biosynthetic intermediates. Biomol Concepts. 2013 Apr;4(2):197–211. doi: 10.1515/bmc-2012-0048. PMID: 25436576.; Ozcengiz G, Demain AL. Recent advances in the biosynthesis of penicillins, cephalosporins and clavams and its regulation. Biotechnol Adv. 2013 Mar;31(2):287–311. doi: 10.1016/j.biotechadv.2012.12.001. PMID: 23228980.; Fernández-Aguado M, Ullán RV, Teijeira F, Rodríguez-Castro R, Martín JF. The transport of phenylacetic acid across the peroxisomal membrane is mediated by the PaaT protein in Penicillium chrysogenum. Applied Microbiology and Biotechnology. 2012 Sep 30;97(7):3073–84. doi: 10.1007/s00253-012-4425-1.; Martín J, Ullán RV, García-Estrada C. Role of peroxisomes in the biosynthesis and secretion of ß-lactams and other secondary metabolites. Journal of Industrial Microbiology & Biotechnology. 2011 Dec 11;39(3):367–82. doi: 10.1007/s10295-011-1063-z.; Spröte P, Hynes MJ, Hortschansky P, Shelest E, Scharf DH, Wolke SM, Brakhage AA. Identification of the novel penicillin biosynthesis gene aatB of Aspergillus nidulans and its putative evolutionary relationship to this fungal secondary metabolism gene cluster. Molecular Microbiology. 2008 Sep 25;70(2):445–61. doi: 10.1111/j.1365-2958.2008.06422.x.; Lamas-Maceiras M, Vaca I, Rodríguez E, Casqueiro J, Martín JF. Amplification and disruption of the phenylacetyl-CoA ligase gene of Penicillium chrysogenum encoding an aryl-capping enzyme that supplies phenylacetic acid to the isopenicillin N-acyltransferase. Biochem J. 2006 Apr 01;395(1):147–55. PMID: 16321143; PMCID: PMC1409706.; Fernández FJ, Cardoza RE, Montenegro E, Velasco J, Gutiérrez S, Martín JF. The isopenicillin N acyltransferases of Aspergillus nidulans and Penicillium chrysogenum differ in their ability to maintain the 40-kDa aß heterodimer in an undissociated form. European Journal of Biochemistry. 2003 Apr 11;270(9):1958–68. doi: 10.1046/j.1432-1033.2003.03561.x.; Tobin MB, Cole SC, Kovacevic S, Miller JR, Baldwin JE, Sutherland JD. Acyl-coenzyme A: isopenicillin N acyltransferase from Penicillium chrysogenum: effect of amino acid substitutions at Ser227, Ser230 and Ser309 on proenzyme cleavage and activity. FEMS Microbiol Lett. 1994 Aug 01;121(1):39–46. doi: 10.1111/j.1574-6968.1994.tb07073.x. PMID: 8082826.; Tobin MB, Baldwin JE, Cole SC, Miller JR, Skatrud PL, Sutherland JD. The requirement for subunit interaction in the production of Penicillium chrysogenum acyl-coenzyme A:isopenicillin N acyltransferase in Escherichia coli. Gene. 1993 Oct 15;132(2):199–206. doi: 10.1016/0378-1119(93)90196-a. PMID: 8224864.; Aplin RT, Baldwin JE, Roach PL, Robinson CV, Schofield CJ. Investigations into the post-translational modification and mechanism of isopenicillin N:acyl-CoA acyltransferase using electrospray mass spectrometry. Biochem J. 1993 Sep 01;294 ( Pt 2)():357–63. PMID: 8396910; PMCID: PMC1134462.; ALVAREZ E, MEESSCHAERT B, MONTENEGRO E, GUTIÉRREZ S, DÍEZ B, BARREDO JL, MARTÍN JF. The isopenicillin-N acyltransferase of Penicillium chrysogenum has isopenicillin-N amidohydrolase, 6-aminopenicillanic acid acyltransferase and penicillin amidase activities, all of which are encoded by the single penDE gene. European Journal of Biochemistry. 1993 Jul;215(2):323–32. doi: 10.1111/j.1432-1033.1993.tb18038.x.; Aplin RT, Baldwin JE, Cole SC, Sutherland JD, Tobin MB. On the production of alpha, beta-heterodimeric acyl-coenzyme A: isopenicillin N-acyltransferase of Penicillium chrysogenum. Studies using a recombinant source. FEBS Lett. 1993 Mar 15;319(1-2):166–70. doi: 10.1016/0014-5793(93)80060-8. PMID: 8384123.; Müller WH, Bovenberg RAL, Groothuis MH, Kattevilder F, Smaal EB, Van der Voort LHM, Verkleij AJ. Involvement of microbodies in penicillin biosynthesis. Biochimica et Biophysica Acta (BBA) - General Subjects. 1992 Apr;1116(2):210–3. doi: 10.1016/0304-4165(92)90118-e.; Demain AL. Production of beta-lactam antibiotics and its regulation. Proc Natl Sci Counc Repub China B. 1991 Oct;15(4):251–65. PMID: 1815263.; Tobin MB, Fleming MD, Skatrud PL, Miller JR. Molecular characterization of the acyl-coenzyme A:isopenicillin N acyltransferase gene (penDE) from Penicillium chrysogenum and Aspergillus nidulans and activity of recombinant enzyme in Escherichia coli. J Bacteriol. 1990 Oct;172(10):5908–14. doi: 10.1128/jb.172.10.5908-5914.1990.; Díez B, Gutiérrez S, Barredo JL, van Solingen P, van der Voort LH, Martín JF. The cluster of penicillin biosynthetic genes. Identification and characterization of the pcbAB gene encoding the alpha-aminoadipyl-cysteinyl-valine synthetase and linkage to the pcbC and penDE genes. Journal of Biological Chemistry. 1990 Sep;265(27):16358–65. doi: 10.1016/s0021-9258(17)46231-4.; Montenegro E, Barredo JL, Gutiérrez S, Díez B, Alvarez E, Martín JF. Cloning, characterization of the acyl-CoA : 6-amino penicillanic acid acyltransferase gene of Aspergillus nidulans and linkage to the isopenicillin N synthase gene. Molecular Genetics and Genomics. 1990 May;221(3):322–30. doi: 10.1007/bf00259395.; Whiteman PA, Abraham EP, Baldwin JE, Fleming MD, Schofield CJ, Sutherland JD, Willis AC. Acyl coenzyme A: 6-aminopenicillanic acid acyltransferase from Penicillium chrysogenum and Aspergillus nidulans. FEBS Letters. 1990 Mar 26;262(2):342–4. doi: 10.1016/0014-5793(90)80224-7.; Barredo JL, van Solingen P, Díez B, Alvarez E, Cantoral JM, Kattevilder A, Smaal EB, Groenen MA, Veenstra AE, Martín JF. Cloning and characterization of the acyl-coenzyme A: 6-aminopenicillanic-acid-acyltransferase gene of Penicillium chrysogenum. Gene. 1989 Nov 30;83(2):291–300. doi: 10.1016/0378-1119(89)90115-7. PMID: 2555269.; Alvarez E, Cantoral JM, Barredo JL, Díez B, Martín JF. Purification to homogeneity and characterization of acyl coenzyme A:6-aminopenicillanic acid acyltransferase of Penicillium chrysogenum. Antimicrob Agents Chemother. 1987 Nov;31(11):1675–82. PMID: 2829713; PMCID: PMC175019.; BATCHELOR FR, DOYLE FP, NAYLER JH, ROLINSON GN. Synthesis of penicillin: 6-aminopenicillanic acid in penicillin fermentations. Nature. 1959 Jan 24;183(4656):257–8. doi: 10.1038/183257b0. PMID: 13622762. |
| superpathway of phenylethylamine degradation Accession ID: BioCyc:META_PWY-6071 |
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Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14390–5. PMID: 20660314; PMCID: PMC2922514.; Hanlon SP, Hill TK, Flavell MA, Stringfellow JM, Cooper RA. 2-phenylethylamine catabolism by Escherichia coli K-12: gene organization and expression. Microbiology (Reading). 1997 Feb;143 ( Pt 2)():513–8. doi: 10.1099/00221287-143-2-513. PMID: 9043126.; Parrott S, Jones S, Cooper RA. 2-Phenylethylamine catabolism by Escherichia coli K12. J Gen Microbiol. 1987 Feb;133(2):347–51. doi: 10.1099/00221287-133-2-347. PMID: 3309152. |
| phenylethylamine degradation I Accession ID: BioCyc:ECO_2PHENDEG-PWY |
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Parrott S, Jones S, Cooper RA. 2-Phenylethylamine catabolism by Escherichia coli K12. J Gen Microbiol. 1987 Feb;133(2):347–51. doi: 10.1099/00221287-133-2-347. PMID: 3309152. |
| phenylacetate degradation I (aerobic) Accession ID: BioCyc:ECO_PWY0-321 |
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Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14390–5. PMID: 20660314; PMCID: PMC2922514.; Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher A, Fuchs G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur J Biochem. 2003 Jul;270(14):3047–54. doi: 10.1046/j.1432-1033.2003.03683.x. PMID: 12846838.; Ferrández A, Miñambres B, García B, Olivera ER, Luengo JM, García JL, Díaz E. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J Biol Chem. 1998 Oct 02;273(40):25974–86. doi: 10.1074/jbc.273.40.25974. PMID: 9748275.; Cooper RA, Jones DC, Parrott S. Isolation and mapping of Escherichia coli K12 mutants defective in phenylacetate degradation. J Gen Microbiol. 1985 Oct;131(10):2753–7. doi: 10.1099/00221287-131-10-2753. PMID: 3906029. |
| phenylacetate degradation II (anaerobic) Accession ID: BioCyc:TRYPANO_PWY-1341 |
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| L-phenylalanine degradation II (anaerobic) Accession ID: BioCyc:AGRO_ANAPHENOXI-PWY |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:SCO_PWY0-321 |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:PCHR_PWY0-321 |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:ECOL316407_PWY0-321 |
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| phenylethylamine degradation I Accession ID: BioCyc:ECOL413997_2PHENDEG-PWY |
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| phenylalanine degradation IV (mammalian, via side chain) Accession ID: BioCyc:THAPS_PWY-6318 |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:META_PWY0-321 |
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Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14390–5. PMID: 20660314; PMCID: PMC2922514. |
| phenylethylamine degradation I Accession ID: BioCyc:META_2PHENDEG-PWY |
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Parrott S, Jones S, Cooper RA. 2-Phenylethylamine catabolism by Escherichia coli K12. J Gen Microbiol. 1987 Feb;133(2):347–51. doi: 10.1099/00221287-133-2-347. PMID: 3309152. |
| phenylethylamine degradation II Accession ID: BioCyc:META_PWY-6534 |
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Arias S, Olivera ER, Arcos M, Naharro G, Luengo JM. Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U. Environmental Microbiology. 2007 Dec 27;10(2):413–32. doi: 10.1111/j.1462-2920.2007.01464.x. |
| phenylalanine degradation II (anaerobic) Accession ID: BioCyc:TRYPANO_ANAPHENOXI-PWY |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:MTBCDC1551_PWY0-321 |
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| phenylacetate degradation I (aerobic) Accession ID: BioCyc:ECOL199310_PWY0-321 |
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| L-phenylalanine degradation II (anaerobic) Accession ID: BioCyc:SCO_ANAPHENOXI-PWY |
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| phenylacetate degradation II (anaerobic) Accession ID: BioCyc:SCO_PWY-1341 |
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