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Escherichia coli K-12 substr. MG1655 Pathway: biotin biosynthesis I

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Genetic Regulation Schematic: ?

Synonyms: vitamin H biosynthesis

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Vitamins Biosynthesis Biotin Biosynthesis
Superpathways

Summary:
Biotin is an essential cofactor for carboxyl group transfer enzymes such as acetyl-CoA carboxylase, and is required by all forms of life [Neidhardt96].

Despite the importance and prevalance of biotin, its detailed biosynthetic pathway remained enigmatic for over 70 years. The first complete pathway for biotin synthesis was suggested for its synthesis in E. coli [Lin10].

Biotin consists of two fused heterocyclic rings and a pentanoate side chain, derived from a pimelate-like structure. The early steps of the pathway, which are described here, describe the synthesis of the precursor of the pimelate moiety. The late steps of the pathway, which are responsible for forming the two rings in the structure of biotin, are described in biotin biosynthesis from 8-amino-7-oxononanoate I.

The origins of the biotin carbon atoms in E. coli are known from 13C NMR analysis of products labeled in vivo [Ifuku94, Sanyal94]. The C3, C5 and C7 carbons are derived from carbon C1 of acetate, while the C2, C4 and C6 carbons are derived from carbon C2 of acetate. The C1 carbon originates from CO2. This labeling pattern indicated that the pimeloyl moiety of biotin is formed by head-to-tail incorporation of three intact acetate units, similar to the synthesis of fatty acids [Sanyal94]. As the biotin C1 and C7 atoms show different labeling patterns, free pimelic acid (a symmetrical molecule) could not be an intermediate, and thus it has been assumed that pimeloyl-CoA is the precursor [Webb07].

The elucidation of the pathway proved difficult, mostly since only two genes, bioC and bioH, were implicated in the synthesis of the pimeloyl moiety [Cleary72, Lemoine96, Rolfe68]. Based on these finding, there have been several suggestions that enzymes of the fatty acid biosynthesis pathway are involved, although none of these suggestions could explain the full process [Sanyal94, Lezius63]. An inclusive model was finally suggested in 2010 [Lin10] and later refined. Based on this model, BioC converts the free carboxyl group of a malonyl-[acp] to its methyl ester by transfer of a methyl group from S-adenosyl-L-methionine [Lin12b]. The newly acquired methyl group mimics the methyl ends of normal fatty acyl chains, and enables the esterified a malonyl-[acp] methyl ester to enter the fatty acid synthetic pathway.

Two reiterations of the fatty acid elongation cycle (see fatty acid elongation -- saturated) produce pimeloyl-[acp] methyl ester, which is cleaved by BioH to give pimeloyl-[acp]. The [acp] protein is then removed in a complex reaction catalyzed by BioF, forming 8-amino-7-oxononanoate, the first intermediate in biotin ring assembly.

The next step in the pathway involves the unusual use of the common methyl-group donor S-adenosyl-L-methionine as an amino-group donor, a reaction catalyzed by 7,8-diaminopelargonic acid synthase [Stoner75a, Stoner75, Eliot02]. The product of this reaction, 7,8-diaminopelargonate, is the target of a unique carboxylase, dethiobiotin synthetase. This enzyme catalyzes the first ring closure by a carboxylation reaction that does not require biotin as a prosthetic group, forming dethiobiotin [Krell70].

The ultimate step in the pathway is catalyzed by biotin synthase. This enzyme inserts a sulfur atom between C6 and C9 of dethiobiotin in a S-adenosyl-L-methionine-dependent reaction. It has not been possible to reconstitute a catalytic reaction of this enzyme in vitro, and there is some uncertainty regarding the reaction mechanism, cofactor requirements, and the source of the sulfur atom [Jarrett05]. However, recent experiments have suggested that a [2Fe-2S] iron-sulfur cluster of the enzyme is the source of the sulfur atom. Consistent with its proposed role as the sulfur donor, degradation of the [2Fe-2S] cluster [Jameson04] as well as exchange of sulfur atoms between the [2Fe-2S] and [4Fe-4S] clusters [Tse06] is observed during turnover of the enzyme.

According to this model, the introduction of the methyl ester early in the pathway disguises the biotin synthetic intermediates so that they become substrates for the fatty acid synthetic pathway. When the synthesis of the pimeloyl moiety is complete and disguise is no longer needed, the methyl group is removed to free the carboxyl group that will eventually be used to attach biotin to its target metabolic enzymes.

An in vitro system that uses dialyzed cell extracts was used in combination with several mutant strains and purified proteins to verify the proposed pathway [Lin10].

Subpathways: biotin biosynthesis from 8-amino-7-oxononanoate I , 8-amino-7-oxononanoate biosynthesis I

Credits:
Created 18-Aug-2010 by Caspi R , SRI International
Revised 08-Nov-2012 by Keseler I , SRI International


References

Cleary72: Cleary PP, Campbell A (1972). "Deletion and complementation analysis of biotin gene cluster of Escherichia coli." J Bacteriol 112(2);830-9. PMID: 4563978

Eliot02: Eliot AC, Sandmark J, Schneider G, Kirsch JF (2002). "The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation." Biochemistry 41(42);12582-9. PMID: 12379100

Ifuku94: Ifuku O, Miyaoka H, Koga N, Kishimoto J, Haze S, Wachi Y, Kajiwara M (1994). "Origin of carbon atoms of biotin. 13C-NMR studies on biotin biosynthesis in Escherichia coli." Eur J Biochem 220(2);585-91. PMID: 8125118

Jameson04: Jameson GN, Cosper MM, Hernandez HL, Johnson MK, Huynh BH (2004). "Role of the [2Fe-2S] cluster in recombinant Escherichia coli biotin synthase." Biochemistry 43(7);2022-31. PMID: 14967042

Jarrett05: Jarrett JT (2005). "Biotin synthase: enzyme or reactant?." Chem Biol 12(4);409-10. PMID: 15850974

Krell70: Krell K, Eisenberg MA (1970). "The purification and properties of dethiobiotin synthetase." J Biol Chem 1970;245(24);6558-66. PMID: 4921568

Lemoine96: Lemoine Y, Wach A, Jeltsch JM (1996). "To be free or not: the fate of pimelate in Bacillus sphaericus and in Escherichia coli." Mol Microbiol 19(3);645-7. PMID: 8830257

Lezius63: Lezius A, Ringelmann E, Lynen F (1963). "[On the biochemical function of biotin. IV. The biosynthesis of biotin.]." Biochem Z 336;510-25. PMID: 13930373

Lin10: Lin S, Hanson RE, Cronan JE (2010). "Biotin synthesis begins by hijacking the fatty acid synthetic pathway." Nat Chem Biol 6(9);682-8. PMID: 20693992

Lin12b: Lin S, Cronan JE (2012). "The BioC O-Methyltransferase Catalyzes Methyl Esterification of Malonyl-Acyl Carrier Protein, an Essential Step in Biotin Synthesis." J Biol Chem. PMID: 22965231

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Rolfe68: Rolfe B, Eisenberg MA (1968). "Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12." J Bacteriol 96(2);515-24. PMID: 4877129

Sanyal94: Sanyal, I, Lee, SL, Flint, DH (1994). "Biosynthesis of pimeloyl-CoA, a biotin precursor in Escherichia coli, follows a modified fatty acid synthesis pathway: 13C-labeling studies." J. Am. Chem. Soc. 116(6):2637-2638.

Stoner75: Stoner GL, Eisenberg MA (1975). "Biosynthesis of 7, 8-diaminopelargonic acid from 7-keto-8-aminopelargonic acid and S-adenosyl-L-methionine. The kinetics of the reaction." J Biol Chem 1975;250(11);4037-43. PMID: 1092682

Stoner75a: Stoner GL, Eisenberg MA (1975). "Purification and properties of 7, 8-diaminopelargonic acid aminotransferase." J Biol Chem 1975;250(11);4029-36. PMID: 1092681

Tse06: Tse Sum Bui B, Mattioli TA, Florentin D, Bolbach G, Marquet A (2006). "Escherichia coli biotin synthase produces selenobiotin. Further evidence of the involvement of the [2Fe-2S]2+ cluster in the sulfur insertion step." Biochemistry 45(11);3824-34. PMID: 16533066

Webb07: Webb, M.E., Marquet, A., Mendel, R.R., Rebeille, F., Smith, A.G (2007). "Elucidating biosynthetic pathways for vitamins and cofactors." Nat. Prod. Rep. 24:988-1008.

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

AbdelHamid07a: Abdel-Hamid AM, Cronan JE (2007). "In vivo resolution of conflicting in vitro results: synthesis of biotin from dethiobiotin does not require pyridoxal phosphate." Chem Biol 14(11);1215-20. PMID: 18022560

Agarwal12: Agarwal V, Lin S, Lukk T, Nair SK, Cronan JE (2012). "Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis." Proc Natl Acad Sci U S A 109(43);17406-11. PMID: 23045647

Alexeev94: Alexeev D, Bury SM, Boys CW, Turner MA, Sawyer L, Ramsey AJ, Baxter HC, Baxter RL (1994). "Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis." J Mol Biol 1994;235(2);774-6. PMID: 8289297

Alexeev94a: Alexeev D, Baxter RL, Sawyer L (1994). "Mechanistic implications and family relationships from the structure of dethiobiotin synthetase." Structure 2(11);1061-72. PMID: 7881906

Alexeev95: Alexeev D, Baxter RL, Smekal O, Sawyer L (1995). "Substrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study." Structure 3(11);1207-15. PMID: 8591031

Alexeev98: Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L (1998). "The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme." J Mol Biol 1998;284(2);401-19. PMID: 9813126

Allison38: Allison, F. E., Minor, F. W. (1938). "Coenzyme R requirements of rhizobia." Soil Sc.i 46:473-483.

Baldock96: Baldock C, Rafferty JB, Sedelnikova SE, Baker PJ, Stuitje AR, Slabas AR, Hawkes TR, Rice DW (1996). "A mechanism of drug action revealed by structural studies of enoyl reductase." Science 274(5295);2107-10. PMID: 8953047

Baxter94: Baxter RL, Ramsey AJ, McIver LA, Baxter HC (1994). "Mechanism of Dethiobiotin Synthetase -- Characterisation of the 8-Aminocarbamate of (7R,8S)-7,8 Diaminononanoate as an Enzyme-bound Intermediate." J Chem Soc Chem Comm (1994);559-560.

Benda02: Benda R, Tse Sum Bui B, Schunemann V, Florentin D, Marquet A, Trautwein AX (2002). "Iron-sulfur clusters of biotin synthase in vivo: a Mossbauer study." Biochemistry 41(50);15000-6. PMID: 12475249

Bergler92: Bergler H, Hogenauer G, Turnowsky F (1992). "Sequences of the envM gene and of two mutated alleles in Escherichia coli." J Gen Microbiol 1992;138 ( Pt 10);2093-100. PMID: 1364817

Bergler94: Bergler H, Wallner P, Ebeling A, Leitinger B, Fuchsbichler S, Aschauer H, Kollenz G, Hogenauer G, Turnowsky F (1994). "Protein EnvM is the NADH-dependent enoyl-ACP reductase (FabI) of Escherichia coli." J Biol Chem 1994;269(8);5493-6. PMID: 8119879

Bergler96: Bergler H, Fuchsbichler S, Hogenauer G, Turnowsky F (1996). "The enoyl-[acyl-carrier-protein] reductase (FabI) of Escherichia coli, which catalyzes a key regulatory step in fatty acid biosynthesis, accepts NADH and NADPH as cofactors and is inhibited by palmitoyl-CoA." Eur J Biochem 242(3);689-94. PMID: 9022698

Berkovitch04: Berkovitch F, Nicolet Y, Wan JT, Jarrett JT, Drennan CL (2004). "Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme." Science 303(5654);76-9. PMID: 14704425

Binkowski05: Binkowski TA, Joachimiak A, Liang J (2005). "Protein surface analysis for function annotation in high-throughput structural genomics pipeline." Protein Sci 14(12);2972-81. PMID: 16322579

Booker07: Booker SJ, Cicchillo RM, Grove TL (2007). "Self-sacrifice in radical S-adenosylmethionine proteins." Curr Opin Chem Biol 11(5);543-52. PMID: 17936058

Breen03: Breen RS, Campopiano DJ, Webster S, Brunton M, Watt R, Baxter RL (2003). "The mechanism of 7,8-diaminopelargonate synthase; the role of S-adenosylmethionine as the amino donor." Org Biomol Chem 1(20);3498-9. PMID: 14599009

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Broach06: Broach RB, Jarrett JT (2006). "Role of the [2Fe-2S]2+ cluster in biotin synthase: mutagenesis of the atypical metal ligand arginine 260." Biochemistry 45(47);14166-74. PMID: 17115711

Bui98: Bui BT, Florentin D, Fournier F, Ploux O, Mejean A, Marquet A (1998). "Biotin synthase mechanism: on the origin of sulphur." FEBS Lett 1998;440(1-2);226-30. PMID: 9862460

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc13.