Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis

Abstract

Mycobacterium tuberculosis is known to synthesize alpha-, methoxy-, and keto-mycolic acids. We propose a detailed pathway to the biosynthesis of all mycolic acids in M. tuberculosis. Fatty acid synthetase I provides C(20)-S-coenzyme A to the fatty acid synthetase II system (FAS-IIA). Modules of FAS-IIA and FAS-IIB introduce cis unsaturation at two locations on a growing meroacid chain to yield three different forms of cis,cis-diunsaturated fatty acids (intermediates to alpha-, methoxy-, and keto-meroacids). These are methylated, and the mature meroacids and carboxylated C(26)-S-acyl carrier protein enter into the final Claisen-type condensation with polyketide synthase-13 (Pks13) to yield mycolyl-S-Pks13. We list candidate genes in the genome encoding the proposed dehydrase and isomerase in the FAS-IIA and FAS-IIB modules. We propose that the processing of mycolic acids begins by transfer of mycolic acids from mycolyl-S-Pks13 to d-mannopyranosyl-1-phosphoheptaprenol to yield 6-O-mycolyl-beta-d-mannopyranosyl-1-phosphoheptaprenol and then to trehalose 6-phosphate to yield phosphorylated trehalose monomycolate (TMM-P). Phosphatase releases the phosphate group to yield TMM, which is immediately transported outside the cell by the ABC transporter. Antigen 85 then catalyzes the transfer of a mycolyl group from TMM to the cell wall arabinogalactan and to other TMMs to produce arabinogalactan-mycolate and trehalose dimycolate, respectively. We list candidate genes in the genome that encode the proposed mycolyltransferases I and II, phosphatase, and ABC transporter. The enzymes within this total pathway are targets for new drug discovery.

FIG. 1.

Chemical structures of mycolic acids from M. tuberculosis. There are five forms of mycolic acids in M. tuberculosis, illustrated with α-mycolic acid from the H37Ra strain and methoxy- and keto-mycolic acids from M. tuberculosis subsp. hominis strains DT, PN, and C. Both cyclopropane rings in α-mycolic acid have the cis configuration. The methoxy- and keto-mycolic acids can have either the cis or trans configuration on the proximal cyclopropane ring.

FIG. 2.

Reaction sequences I to V in the mycobacterial FAS-I system, leading to the formation of early precursors of mycolic acids. These reactions take place on a single multienzyme complex. HS-Enz, ACP-like protein in the complex; C₄, butyryl; C₂₀, eicosanoyl; C₂₆, hexacosanoyl.

FIG. 3.

Generalized FAS-II elongation module of M. tuberculosis for the synthesis of meroacids. The substrates are R-CO-S-ACP and malonyl-S-ACP derived from malonyl-S-CoA by FabD. R, long-chain alkyl group. Enzymes involved in these reactions are as follows: 1, β-ketoacyl-ACP synthase (KasA/KasB); 2, β-ketoacyl-ACP reductase; 3, β-hydroxyacyl-ACP dehydrase; 4, 2-trans-enoyl-ACP reductase (InhA). The product of the last reaction undergoes the next cycle of elongation as the ACP derivative on another FAS-II module. This is a long-chain fatty acid elongation system in which the hydrocarbon chain is increased by two carbons with the completion of each cycle. t, trans isomer.

FIG. 4.

Proposed pathway to synthesis of cis,cis-diunsaturated meroacid precursors and α-meroacid. In this illustration, the initial substrates for the FAS-II system are eicosanoyl-S-CoA (derived from FAS-I) and malonyl-S-ACP (derived from malonyl-S-CoA by FabD). Enzymes involved in these reactions are as follows: 1, β-ketoacyl-ACP synthase-III; 6, β-ketoacyl-ACP synthase (Kas); 2 and 7, β-ketoacyl-ACP reductase; 3 and 8, β-hydroxyacyl-ACP dehydrase; 4 and 9, 2-trans-enoyl-ACP isomerase; 5 and 10, elongation (e) by multiple FAS-II modules; 11, cyclopropane synthase (cp). The FAS-IIA and FAS-IIB modules are identified in the pathway. t and c, trans and cis isomers, respectively. For the synthesis of α-meroacid, x = 10 and y = 17; for the synthesis of methoxy-meroacid, x = 16 and y = 17; for the synthesis of keto-meroacid, x = 16 and y = 19.

FIG. 5.

Modification of distal and proximal cis unsaturations of cis,cis-diunsaturated meroacid precursors in the pathway to synthesis of oxygenated meroacids. MmaA4 converts the distal cis unsaturation to a secondary alcohol with an adjacent methyl branch. MmaA1 converts the proximal cis unsaturation to an allylic methyl branch with trans unsaturation. SAM is the cofactor in these reactions. t and c, trans and cis isomers, respectively.

FIG. 6.

Methyltransferases and oxidation-reduction (redox) to form the methoxy group of methoxy-meroacids and the oxo group of keto-meroacids on the pathway to synthesis of oxygenated meroacids. MmaA2 introduces the methyl group on the secondary alcohol, MmaA3 introduces the proximal cis-cyclopropane ring, and CmaA2 introduces the proximal trans-cyclopropane ring. Redox is the proposed oxidation-reduction system that converts the secondary alcohol to an oxo group. t and c, trans and cis isomers, respectively.

FIG. 7.

Proposed mechanism of Claisen-type condensation for the synthesis of α-mycolic acid by Pks13 in M. tuberculosis. FadD32 converts the α-meroacyl-S-ACP derived from the FAS-II system to α-meroacyl-AMP. The hexacosanoyl-S-CoA derived from FAS-I is carboxylated by acyl-CoA carboxylases (AccD4 and AccD5) to yield 2-carboxyl-C₂₆-S-CoA. These two products are the substrates for the condensation reaction catalyzed by Pks13. Reaction 1 is the loading step in which the two substrates are covalently attached to Pks13. Reaction 2 is the transfer of a meroacyl group from the N-terminal PPB domain to the condensing enzyme (KS). Reactions 3 and 4 together are the condensation step and reduction of the 3-oxo group to the secondary alcohol by an unidentified reductase to yield the mature α-mycolate. Domains of Psk13 are the two nonequivalent PPB domains (signature motif of ACP), KS domain, AT domain, and TE domain.

FIG. 8.

Processing of newly synthesized mycolic acids in M. tuberculosis. Inside the cell, newly synthesized mycolic acid in thioester linkage to the near-C-terminal PPB domain of Pks13 is transferred first to man-P-heptaprenol to yield Myc-PL and then to trehalose 6-phosphate to yield TMM-P. Dephosphorylation of this product yields TMM. TMM is then transported outside the cell (outer membrane) by a proposed TMM transporter (ABC transporter cassette), where it is involved in the synthesis of both TDM and cell wall arabinogalactan-mycolate. Reactions: 1, mycolyltransferase I; 2, mycolyltransferase II; 3, TMM-P phosphatase; 4, TMM transporter; 5 and 6, Ag85 as the mycolyltransferase (FbpA, FbpB, and FbpC). man-P-heptaprenol, mannosyl-phosphoryl-heptaprenol; treh, trehalose; AG, arabinogalactan; AG-M, arabinogalactan-mycolate.

FIG. 9.

Sequence alignment of the proposed M. tuberculosis β-hydroxy-acyl-ACP dehydrase FabZ (Rv0098) with E. coli CFT073 FabZ (AAN78709), S. pneumoniae FabZ (NC_003028, SP0424 open reading frame), and E. coli CFT073 FabA (AAN79558). Multiple-sequence alignments were obtained with the Clustal W program (version 1.8) (106). Active-site residues His and Glu are indicated by asterisks. Black shading indicates identical residues; gray shading indicates similar residues. Hyphens represent gaps introduced to maintain the alignment. For better visualization, the first 23 residues of E. coli FabA are not included in the alignment, because none of them matched in the comparison.

FIG. 10.

Sequence alignment of the proposed M. tuberculosis 2-trans-enoyl-acyl-ACP isomerases FabM (EchA10 and EchA11) with S. pneumoniae FabM (NC_003028, SP0415 open reading frame). Multiple-sequence alignments were obtained with the Clustal W program (version 1.8) (106). Active-site residue Asp is indicated by an asterisk. Black shading indicates identical residues; gray shading indicates similar residues. Hyphens represent gaps introduced to maintain the alignment.

FIG. 11.

Functional links and operon inference for a region involved in the biosynthesis of mycolic acid. Inference of Rv3802c protein function and operon organization is based on a combined computational approach (99). OP, operon method; RS, Rosetta Stone method; PP, phylogenetic profile method; GN, conserved gene neighbor method.

FIG. 12.

Sequence of the proposed mycolyltransferase II (Rv1288) from M. tuberculosis. (A) Schematic presentation of Rv1288. The N-terminal LysM repeats are named I to III. The esterase D domain of the protein is located within the N-terminal amino acids 73 to 443 of the protein. AA, amino acids. (B) Amino acid sequence alignment of repeated N-terminal LysM motifs I to III of Rv1288 plus intervening sequences. Asterisks indicate the consensus sequence proposed by Joris et al. (46). (C) Amino acid sequence alignment of Rv1288 with mycolyltransferases (FbpA, FbpB, and FbpC). Active-site residues Ser, Glu, and His are indicated by asterisks. For better visualization, the first 78 residues of Rv1288 are not included in the alignment, because none of them matched in the comparison. The CLUSTAL W program (version 1.81) (106) was used for multiple-sequence alignment. Black shading indicates identical residues; gray shading indicates similar residues.

FIG. 13.

Sequence alignment of Rv0774c and Rv0519c (proposed mycolyltransferase II) with FbpA, FbpB, and FbpC (mycolyltransferases). At the top of the alignments, active-site residues Ser, Asp/Glu, and His are indicated by asterisks. Multiple-sequence alignments were obtained with the Clustal W program (version 1.8) (106), and the resulting alignment was refined manually. Black shading indicates residues identical to those in mycolyltransferases; gray shading indicates residues similar to those in mycolyltransferases. For better visualization, the first 78 residues of Rv1288 are not included in the alignment, because none of them matched in the comparison.

FIG. 14.

Sequence alignment of the proposed TMM-6-phosphate phosphatase (Rv3400 and Rv2006 N-terminal haloacid dehalogenase-like hydrolase) with trehalose-6-phosphate phosphatases OtsB1 (Rv2006 trehalose phosphatase domain) and OtsB2 (Rv3372). At the top of the alignments, the conserved domain is indicated. Multiple-sequence alignments were obtained with the Clustal W program (version 1.8) (106). Black shading indicates residues identical to those in OtsB1 and OtsB2; gray shading indicates residues similar to those in OtsB1 and OtsB2.