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MetaCyc Pathway: mycolate biosynthesis
Inferred from experiment

Pathway diagram: mycolate biosynthesis

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

Superclasses: BiosynthesisFatty Acid and Lipid BiosynthesisFatty Acid Biosynthesis

Some taxa known to possess this pathway include : Mycobacterium tuberculosis H37Rv

Expected Taxonomic Range: Mycobacteriaceae

General Background

Mycolic acids are the hallmark of the cell envelope of Mycobacterium tuberculosis and related species and genera. They comprise a homologous series of C60-C90 (2R)-alkyl-(3R)-hydroxy very long-chain fatty acids, and are found as either esters of an arabinogalactan or as free lipids in the form of trehalose dimycolate (TDM). Both forms contribute to forming the two leaflets of the mycobacterial outer membrane, also called the mycomembrane, which protects the organism from antibiotics and the host's immune system [Takayama05, Bhatt07a, Schweizer04].

There is a significant variability in the structure of mycolic acids among different species. Acids from Corynebacterium species contain 22-38 carbon atoms, Hoyosella and Amycolicicoccus spp. contain 30-36, Dietzia spp. contain 34-38, Rhodococcus spp. contain 34-52 in, Nocardia spp. contain 46-60, Gordonia spp. contain 46-66, Tsukamurella spp. contain 64-78 , Mycobacterium spp. contain 60-90, and Segniliparus spp. contain up to 100 carbon atoms [Marrakchi14].

The acids are formed by a Claisen-type condensation of two components - the meromycolic chain and a fatty acid. Several structural classes of mycolic acids exist. In Mycobacterium tuberculosis the most apolar ones, known as α-mycolic acids, contain 74-80 carbon atoms (out of which 22-26 carbons are located in the fatty acid moiety and the rest on the mero-chain) and generally two double bonds (that can be in either cis- or trans-configuration) or two cis-cyclopropyl groups located in the meromycolic chain. The cyclopropane rings are believed to protect the organism from oxidative stress [Takayama05]. α-Mycolic acids usually comprise more than 70 percent of the total mycolic acids in the cell.

Other classes are defined by additional oxygen functions located in the distal part of the meromycolic chain, and include keto-, methoxy-, wax ester-, epoxy-, and hydroxy-types. In Mycobacterium tuberculosis the oxygenated mycolic acids (keto-, methoxy-, and hydroxy-types) contain ~84-88 carbon atoms, and are thus four to six carbons longer than the α-mycolic acids from the same strains.

About This Pathway

The biosynthesis of mycolic acids could be divided conceptually into three parts: the biosynthesis of the fatty acid moiety, the biosynthesis of the mero-acid moiety, and the condensation of both parts.

The fatty acid moiety is produced by a "eukaryotic-like" multifunctional FAS-I enzyme complex (encoded by the Rv2524C gene), which produces C24-C26 acids (lignocerotate and cerotate), which are used as the "α branch" of the mycolic acids following carboxylation at position 2.

At the level of C22 ( trans-docos-2-enoyl-[acp]) an isomerase encoded by echA10 or echA11 acts on some of the acids, transferring the double bond at position 2, which is introduced by the fatty acid dehydratase domain, to position 3. While those acids that were not affected by the isomerase continue elongation by FAS-I to the level of C26, the desaturated acid that result from isomerization, trans-docos-3-enoyl-[acp], is no longer recognized by the FAS I enzyme. Instead, it is processed by a second, bacterial-like FAS-II system, which is composed of multiple discrete soluble enzymes (encoded by kasA/ kasB, fabG1, meromycolic acid 3-hydroxyacyl-[acyl-carrier-protein] dehydratase I/ meromycolic acid 3-hydroxyacyl-[acyl-carrier-protein] dehydratase II, and inhA. The longer fatty acids generated by FAS II eventually form the mero-chain moieties of the mycolic acids.

Although the two FAS systems differ in their molecular organizations, substrates, and carrier specificities, they share the typical reaction sequence, with an iterative series of reactions built on successive additions of a two-carbon unit from malonyl-CoA (FAS I) or malonyl-[acp] (FAS II) to the nascent acyl group.

During elongation by the FAS-II system, continuous introduction of 2-carbon units upstream of the the double bond at position 3 results in its "migration" farther from the carboxylate (to positions 5, 7, 9 etc). At the level of C35 the isomerase (encoded by echA10 or echA11) acts again, shifting another double bond from position 2 to position 3. This action of the isomerase results in a second branch in the pathway, where some of the acids continue with an additional double bond, while others continue without it. Both continue to be elongated by the FAS-II system. The acids that escaped the isomeization at the C35 level undergo an isomerization at the level of C40. This isomerization event does not result in a branch in the pathway.

Following completion of the elongation process, the acids are modified by several additional enzymes which introduce methoxy groups and convert double bonds to cyclopropyl groups (including mmaA1, mmaA2, mmaA3, mmaA4, pcaA, cmaA2). The final modified acids, as well as the final product of the FAS-I system, are then transferred from their [acp] and CoA carriers (respectively) to a polyketide enzyme, encoded by the pks13 gene, which catalyzes their condensation into a mycolic acid [Portevin04, Trivedi04].

Additional enzymes catalyze the conjugation of the mycolic acids first to D-mannopyranosyl-1-phosphoheptaprenol and subsequently to α,α-trehalose 6-phosphate. Following the removal of the phosphate, the free mycolic acid is exported to the periplasm, where it is attached to arabinogalactan in the cell wall, or to a second mycolic acid, forming a dimycolate.

Superpathways: superpathway of mycolate biosynthesis

Created 02-Dec-2008 by Sarker M, SRI International
Revised 20-Feb-2014 by Caspi R, SRI International


Azuma69: Azuma I, Yamamura Y, Misaki A (1969). "Isolation and characterization of arabinose mycolate from firmly bound lipids of mycobacteria." J Bacteriol 98(1);331-3. PMID: 4976469

Bhatt07a: Bhatt A, Molle V, Besra GS, Jacobs WR, Kremer L (2007). "The Mycobacterium tuberculosis FAS-II condensing enzymes: their role in mycolic acid biosynthesis, acid-fastness, pathogenesis and in future drug development." Mol Microbiol 64(6);1442-54. PMID: 17555433

Marrakchi14: Marrakchi H, Laneelle MA, Daffe M (2014). "Mycolic acids: structures, biosynthesis, and beyond." Chem Biol 21(1);67-85. PMID: 24374164

Portevin04: Portevin D, De Sousa-D'Auria C, Houssin C, Grimaldi C, Chami M, Daffe M, Guilhot C (2004). "A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms." Proc Natl Acad Sci U S A 101(1);314-9. PMID: 14695899

Schweizer04: Schweizer E, Hofmann J (2004). "Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems." Microbiol Mol Biol Rev 68(3);501-17. PMID: 15353567

Steck78: Steck PA, Schwartz BA, Rosendahl MS, Gray GR (1978). "Mycolic acids. A reinvestigation." J Biol Chem 253(16);5625-9. PMID: 97301

Takayama05: Takayama K, Wang C, Besra GS (2005). "Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis." Clin Microbiol Rev 18(1);81-101. PMID: 15653820

Trivedi04: Trivedi OA, Arora P, Sridharan V, Tickoo R, Mohanty D, Gokhale RS (2004). "Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria." Nature 428(6981);441-5. PMID: 15042094

Watanabe01a: Watanabe M, Aoyagi Y, Ridell M, Minnikin DE (2001). "Separation and characterization of individual mycolic acids in representative mycobacteria." Microbiology 147(Pt 7);1825-37. PMID: 11429460

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

Alderwick05: Alderwick LJ, Radmacher E, Seidel M, Gande R, Hitchen PG, Morris HR, Dell A, Sahm H, Eggeling L, Besra GS (2005). "Deletion of Cg-emb in corynebacterianeae leads to a novel truncated cell wall arabinogalactan, whereas inactivation of Cg-ubiA results in an arabinan-deficient mutant with a cell wall galactan core." J Biol Chem 280(37);32362-71. PMID: 16040600

Anderson01a: Anderson DH, Harth G, Horwitz MA, Eisenberg D (2001). "An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase." J Mol Biol 307(2);671-81. PMID: 11254389

Arguelles00: Arguelles JC (2000). "Physiological roles of trehalose in bacteria and yeasts: a comparative analysis." Arch Microbiol 174(4);217-24. PMID: 11081789

Badell09: Badell E, Nicolle F, Clark S, Majlessi L, Boudou F, Martino A, Castello-Branco L, Leclerc C, Lewis DJ, Marsh PD, Gicquel B, Winter N (2009). "Protection against tuberculosis induced by oral prime with Mycobacterium bovis BCG and intranasal subunit boost based on the vaccine candidate Ag85B-ESAT-6 does not correlate with circulating IFN-gamma producing T-cells." Vaccine 27(1);28-37. PMID: 18977269

Belisle97: Belisle JT, Vissa VD, Sievert T, Takayama K, Brennan PJ, Besra GS (1997). "Role of the major antigen of Mycobacterium tuberculosis in cell wall biogenesis." Science 276(5317);1420-2. PMID: 9162010

Bhamidi08: Bhamidi S, Scherman MS, Rithner CD, Prenni JE, Chatterjee D, Khoo KH, McNeil MR (2008). "The identification and location of succinyl residues and the characterization of the interior arabinan region allow for a model of the complete primary structure of Mycobacterium tuberculosis mycolyl arabinogalactan." J Biol Chem 283(19);12992-3000. PMID: 18303028

Bhatt07: Bhatt A, Fujiwara N, Bhatt K, Gurcha SS, Kremer L, Chen B, Chan J, Porcelli SA, Kobayashi K, Besra GS, Jacobs WR (2007). "Deletion of kasB in Mycobacterium tuberculosis causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice." Proc Natl Acad Sci U S A 104(12);5157-62. PMID: 17360388

Bhatt08: Bhatt A, Brown AK, Singh A, Minnikin DE, Besra GS (2008). "Loss of a mycobacterial gene encoding a reductase leads to an altered cell wall containing beta-oxo-mycolic acid analogs and accumulation of ketones." Chem Biol 15(9);930-9. PMID: 18804030

Boissier06: Boissier F, Bardou F, Guillet V, Uttenweiler-Joseph S, Daffe M, Quemard A, Mourey L (2006). "Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in Mycobacterium tuberculosis." J Biol Chem 281(7);4434-45. PMID: 16356931

Braibant00: Braibant M, Gilot P, Content J (2000). "The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis." FEMS Microbiol Rev 24(4);449-67. PMID: 10978546

Brown07a: Brown AK, Bhatt A, Singh A, Saparia E, Evans AF, Besra GS (2007). "Identification of the dehydratase component of the mycobacterial mycolic acid-synthesizing fatty acid synthase-II complex." Microbiology 153(Pt 12);4166-73. PMID: 18048930

Byers07: Byers DM, Gong H (2007). "Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family." Biochem Cell Biol 85(6);649-62. PMID: 18059524

Cole98: Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998). "Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Nature 393(6685);537-44. PMID: 9634230

Crowe94: Crowe LM, Spargo BJ, Ioneda T, Beaman BL, Crowe JH (1994). "Interaction of cord factor (alpha, alpha'-trehalose-6,6'-dimycolate) with phospholipids." Biochim Biophys Acta 1194(1);53-60. PMID: 8075141

De94: De Wit L, Palou M, Content J (1994). "Nucleotide sequence of the 85B-protein gene of Mycobacterium bovis BCG and Mycobacterium tuberculosis." DNA Seq 4(4);267-70. PMID: 7987013

Dinadayala03: Dinadayala P, Laval F, Raynaud C, Lemassu A, Laneelle MA, Laneelle G, Daffe M (2003). "Tracking the putative biosynthetic precursors of oxygenated mycolates of Mycobacterium tuberculosis. Structural analysis of fatty acids of a mutant strain deviod of methoxy- and ketomycolates." J Biol Chem 278(9);7310-9. PMID: 12473649

Dong15: Dong Y, Li J, Qiu X, Yan C, Li X (2015). "Expression, purification and crystallization of the (3R)-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis." Protein Expr Purif 114;115-120. PMID: 26118698

Edavana04: Edavana VK, Pastuszak I, Carroll JD, Thampi P, Abraham EC, Elbein AD (2004). "Cloning and expression of the trehalose-phosphate phosphatase of Mycobacterium tuberculosis: comparison to the enzyme from Mycobacterium smegmatis." Arch Biochem Biophys 426(2);250-7. PMID: 15158675

Elamin09: Elamin AA, Stehr M, Oehlmann W, Singh M (2009). "The mycolyltransferase 85A, a putative drug target of Mycobacterium tuberculosis: development of a novel assay and quantification of glycolipid-status of the mycobacterial cell wall." J Microbiol Methods 79(3);358-63. PMID: 19857528

Glickman00: Glickman MS, Cox JS, Jacobs WR (2000). "A novel mycolic acid cyclopropane synthetase is required for cording, persistence, and virulence of Mycobacterium tuberculosis." Mol Cell 5(4);717-27. PMID: 10882107

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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