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J Bacteriol. May 2007; 189(9): 3655–3659.
Published online Feb 16, 2007. doi:  10.1128/JB.00040-07
PMCID: PMC1855906

A Riboswitch Regulates Expression of the Coenzyme B12-Independent Methionine Synthase in Mycobacterium tuberculosis: Implications for Differential Methionine Synthase Function in Strains H37Rv and CDC1551[down-pointing small open triangle]


We observed vitamin B12-mediated growth inhibition of Mycobacterium tuberculosis strain CDC1551. The B12 sensitivity was mapped to a polymorphism in metH, encoding a coenzyme B12-dependent methionine synthase. Vitamin B12-resistant suppressor mutants of CDC1551 containing mutations in a B12 riboswitch upstream of the metE gene, which encodes a B12-independent methionine synthase, were isolated. Expression analysis confirmed that the B12 riboswitch is a transcriptional regulator of metE in M. tuberculosis.

Comparative genomics has been profitably utilized to elucidate interstrain variability between Mycobacterium tuberculosis clinical and laboratory isolates (7, 8, 19, 20). Moreover, recent studies (11, 14, 16) have begun to address the next challenge: mapping phenotypic consequences to identified polymorphisms. A whole-genome comparison between H37Rv, a virulent laboratory strain, and the clinical isolate CDC1551 identified a large sequence polymorphism at the PPE37-metH locus in CDC1551 that eliminates 1,196 bp at the 3′ terminus of the metH gene (7) (Fig. (Fig.1).1). MetH is one of two methionine synthases predicted to catalyze the final S-methyl transfer reaction in de novo methionine biosynthesis in M. tuberculosis (4)—the formation of methionine from homocysteine—and requires a vitamin B12-derived cofactor for activity; the other, MetE, does not. Full-length MetH is a monomer comprising four distinct domains (Fig. (Fig.1).1). In CDC1551, 398 amino acids have been lost from the C terminus, partially disrupting the coenzyme B12 (or cobalamin [CBL])-binding domain and eliminating completely the S-adenosyl-l-methionine (SAM)-binding domain, which is required for the reductive reactivation of the B12 moiety in MetH (6).

FIG. 1.
Deletion polymorphism at the PPE37-metH locus of CDC1551. Full-length MetH comprises an N-terminal homocysteine-binding domain (HCY), an N-methyltetrahydrofolate-binding domain (MTH), a CBL-binding domain, and a C-terminal SAM-binding domain (6). A large ...

Little is known about the regulation of corresponding B12-dependent and B12-independent enzymes in M. tuberculosis or their contribution to viability and pathogenesis (5). However, any suggestion of redundant methionine synthase function must be reconciled with the predicted essentiality of metE for optimal growth of M. tuberculosis in vitro (18). In particular, the apparent inability of metH to compensate for the loss of metE raises fundamental questions about the functionality of metH in this organism. Alternatively, the predicted essentiality of metE may indicate an inability of M. tuberculosis to produce the B12 cofactor necessary to enable MetH to function as the sole methionine synthase in vitro, despite encoding an apparently complete vitamin B12 biosynthetic pathway (17).

In genomes containing corresponding B12-dependent and B12-independent enzymes, the activity of the B12-independent enzyme is often subject to regulation by a B12 riboswitch (23). Riboswitches are highly structured domains found within the mRNA of the regulated gene (1). Ligand-specific binding of a small molecule (such as B12) to the riboswitch results in the formation of an alternative RNA structure that attenuates transcription or translation (12). The association of riboswitch-mediated regulation with many essential metabolite biosynthetic and transport pathways has prompted the development of novel antibacterials that target these genetic control elements (2). Two B12 riboswitch motifs have been identified in the M. tuberculosis genome and are located immediately upstream of metE (Fig. (Fig.2)2) and PPE2 (17, 23). Recently, Borovok et al. (3) took advantage of a B12 riboswitch to effect growth arrest in a Streptomyces coelicolor mutant lacking the coenzyme B12-dependent ribonucleotide reductase (RNR) NrdJ. In that case, transcription of the corresponding B12-independent enzyme, NrdAB, was repressed by exogenous B12, effectively abrogating essential RNR function in Streptomyces.

FIG. 2.
Predicted M. tuberculosis metE B12 riboswitch. The secondary structure is drawn according to the scheme presented by Vitreschak et al. (23). Uppercase letters indicate residues identified by Vitreschak et al. (23) to be invariant across approximately ...

We sought to address by genetic means whether metH is functional in M. tuberculosis H37Rv and to investigate the consequences of the deletion polymorphism on the function of metH in CDC1551. Furthermore, the location of a putative riboswitch in the metE promoter region of M. tuberculosis suggested the possibility of exploiting the CDC1551 metH polymorphism to determine whether B12 regulates the activity of metE in M. tuberculosis. In this paper, we describe the results of these investigations.

A metE mutant of M. tuberculosis H37Rv is viable when supplemented with vitamin B12.

To establish the ability of metH to compensate for the loss of metE in M. tuberculosis, we attempted to generate a metE deletion mutant of H37Rv (ΔmetE) (Fig. (Fig.3A)3A) by allelic replacement with a hyg-marked metE deletion allele carried on the suicide plasmid p2ΔmetE17 (see Table S1 in the supplemental material) by previously described methods (9, 15). Consistent with the predicted essentiality of metE (18), a ΔmetE mutant could not be obtained on normal solid medium (Middlebrook 7H10; Difco). However, supplementing the growth medium with vitamin B12 (cyanocobalamin; Sigma) at a concentration of 10 μg/ml enabled the ready isolation of a ΔmetE mutant (Fig. 3B and C). The successful generation of an H37Rv metE mutant on B12-supplemented medium was significant, as it established simultaneously the ability of M. tuberculosis to transport vitamin B12 despite the absence of identifiable B12-specific transporters in the M. tuberculosis genome (17) and the capacity of the organism to convert exogenous vitamin B12 into the methylcobalamin cofactor required for MetH-catalyzed S-methyl transfer (10). It also strongly supported functionality of the metH-encoded gene, although the need to supplement the growth medium suggested that M. tuberculosis was unable to produce sufficient B12 cofactor in vitro to allow MetH to compensate for the loss of function of MetE.

FIG. 3.
Construction and phenotypic characterization of M. tuberculosis methionine synthase mutants. (A) Construction and genotypic characterization of mutant strains. Genomic DNA was digested with the relevant restriction enzyme and probed with either a metE ...

Growth of CDC1551 is inhibited on solid medium containing vitamin B12.

We reasoned that if the truncation in CDC1551 metH rendered this gene nonfunctional, then it should not be possible to construct a CDC1551 metE deletion mutant by the approach described above for H37Rv. Indeed, we were unable to recover a metE mutant of this strain using the knockout vector p2ΔmetE17 (see Table S1 in the supplemental material): 102 white, sucrose-resistant, hygromycin-resistant clones recovered from the two-step allelic exchange procedure (15) were screened by PCR, and all were found to retain the wild-type metE allele. The inability to disrupt metE in CDC1551 thus provided a further indication that its truncated metH gene was not functionally active.

During the course of these experiments, we noticed that wild-type CDC1551 exhibited a marked plating defect on solid medium supplemented with vitamin B12 (Fig. (Fig.3C):3C): at a B12 concentration of 10 μg/ml, a 3 log reduction in CFU was evident (Fig. (Fig.3B).3B). In stark contrast, no effect on H37Rv growth was observed (Fig. 3B and C). These observations suggested that differential methionine synthase function might determine the contrasting growth phenotypes displayed by CDC1551 and H37Rv on Middlebrook 7H10 agar supplemented with B12. That is, an inactivated metH coupled with B12-mediated suppression of metE effectively abrogated all methionine synthase activity in CDC1551, thus preventing growth.

Disruption of metH renders H37Rv sensitive to vitamin B12.

To confirm that the lack of MetH function was directly responsible for the B12 sensitivity of CDC1551, we constructed two independent hyg-marked metH deletion mutants of H37Rv (Fig. (Fig.3A;3A; also see Table S1 in the supplemental material). A 391-bp BglII deletion in H37Rv ΔmetH(B) eliminated 63 amino acids in the CBL domain and 71 amino acids in the SAM domain (Fig. (Fig.1),1), roughly approximating the CDC1551 metH genotype in which 102 amino acids are missing from the CBL domain together with the entire SAM domain. H37Rv ΔmetH(BB), on the other hand, contained a much larger deletion (1,417-bp region spanned by BglII and BclI sites), which eliminated the entire CBL domain and disrupted both the methyltetrahydrofolate and SAM domains (Fig. (Fig.1).1). The ΔmetH(BB) allele was therefore expected to abrogate metH activity completely. Plating both mutants on medium supplemented with vitamin B12 at 10 μg/ml confirmed that disruption of metH indeed renders M. tuberculosis B12 sensitive (Fig. 3B and C). Furthermore, ΔmetH(B) recapitulated precisely the CDC1551 phenotype, indicating that the combined disruption of the CBL and SAM domains is sufficient to render M. tuberculosis MetH nonfunctional. Conversely, by introducing a copy of the full-length H37Rv metH gene into the CDC1551 chromosome, we were able to reverse the B12 sensitivity of CDC1551 (metHKin) (Fig. (Fig.3B3B and and3C).3C). CDC1551 metHKin (Fig. (Fig.3A)3A) is a single-crossover recombinant that carries the full-length H37Rv metH open reading frame plus flanking and vector sequences (p2metHKin) (see Table S1 in the supplemental material), as well as retaining its native truncated metH allele. Together, these observations provided further evidence that CDC1551 MetH was inactive.

Vitamin B12-resistant CDC1551 mutants containing mutated B12 riboswitches.

Colonies of CDC1551 of normal size and morphology arose on B12-containing plates at a frequency of ~ 10−3 (Fig. (Fig.3B).3B). We postulated that a mutation in the B12 riboswitch motif upstream of metE might relieve B12-mediated suppression of metE and so allow growth of these “vitamin B12 suppressor” mutants. To ascertain the heritability of the suppressor phenotype, selected colonies were passaged in liquid medium (Middlebrook 7H9; Difco) without B12 supplement. Restreaking of these cultures onto solid medium supplemented with B12 established that the ability to grow on B12 was not lost after passage (a representative suppressor mutant, B12P2, is shown in Fig. 3B and C). To characterize these mutants genotypically, we sequenced the 500-bp genomic region upstream of metE, which contains the B12 riboswitch in 10 CDC1551 B12 suppressor mutants. We also sequenced 10 B12 suppressor mutants derived from H37Rv ΔmetH(B). This analysis revealed that 2 of the 10 CDC1551 mutants contained a C→T transition in a conserved region of the B12 riboswitch termed the “B12-box” (23). In addition, one H37Rv ΔmetH(B) suppressor mutant contained a C→T transition in an adjacent position within the B12-box (Fig. (Fig.2).2). These data supported the idea that the vitamin B12 plating deficiency of CDC1551 results from B12-mediated repression of metE. However, the mechanism(s) of resistance in the remaining CDC1551 and ΔmetH(B) B12 suppressor isolates remains to be elucidated. Preliminary sequence analysis has failed to reveal any mutations in the only other identified M. tuberculosis B12 riboswitch—located upstream of PPE2 (17)—in these strains. Instead, it is possible that they represent B12 transport mutants with diminished capacity to take up B12.

The B12 riboswitch is a transcriptional regulator of metE.

To determine whether the B12 riboswitch functions as a transcriptional or posttranscriptional regulator of M. tuberculosis metE, we analyzed the expression of metE during growth in liquid medium supplemented with vitamin B12. Expression of the housekeeping gene sigA was used to benchmark relative expression levels, as described previously (5, 13). In both H37Rv and CDC1551, metE transcript levels were significantly reduced in B12-supplemented medium, whereas expression of sigA was unaffected (Fig. (Fig.4).4). In contrast to the repression of metE observed in the parental CDC1551 strain, the expression of metE in the B12P2 mutant was completely unaffected by exogenous B12. This observation confirmed that vitamin B12-mediated repression of metE activity in wild-type M. tuberculosis occurs at the level of transcription. Interestingly, constitutive transcription of metE in the B12P2 mutant was noticeably diminished relative to H37Rv and CDC1551 when standardized against sigA. The B12P2 mutant displayed no growth deficiency under standard conditions in vitro, however, suggesting either that reduced metE expression has no effect on growth or that B12P2 harbors a second-site mutation(s) that ameliorates any growth-inhibitory effect of reduced metE expression.

FIG. 4.
Exogenous vitamin B12 represses transcription of M. tuberculosis metE. Reverse transcription (RT)-PCR analysis of metE expression in strains H37Rv, CDC1551, and the B12 suppressor mutant B12P2 is shown. Cells were grown for 5 h in Sauton's minimal medium ...

Conclusions and implications.

In this study, we took advantage of an identified deletion polymorphism in a clinical isolate to confirm fundamental aspects of M. tuberculosis biology. Specifically, we have presented genetic evidence that both metE and metH encode functional methionine synthases and that transcription of metE is controlled by a B12 riboswitch. In addition, through the construction of a metE deletion mutant of strain H37Rv, we have demonstrated the ability of M. tuberculosis to transport vitamin B12. A previous comparative genomic analysis had situated mycobacteria (including M. tuberculosis) in a rare category of B12-utilizing organisms lacking an identifiable B12-specific transport system (17). Further analysis of those B12 suppressor isolates of CDC1551 and ΔmetH(B) that did not map to the metE-related B12 riboswitch may yield some insight into potential nonorthologous B12 transport systems in M. tuberculosis.

The M. tuberculosis genome contains two other B12-dependent enzymes in addition to metH (4): a class II RNR encoded by nrdZ (5) and a methylmalonyl coenzyme A mutase encoded by mutAB. The proof of functionality of both a B12-dependent enzyme (MetH) and a B12-dependent regulatory mechanism (the B12 riboswitch), therefore, has broader implications for M. tuberculosis pathogenesis. For example, does M. tuberculosis synthesize B12 and, if so, under what conditions? Alternatively, does M. tuberculosis acquire vitamin B12 from the host? In either case, whether host acquired or synthesized de novo, does B12 availability signal a shift in metabolism to the utilization of all three B12-dependent enzymes? Also, given the presence of only two B12 riboswitches in the M. tuberculosis genome, how is flux through the remaining B12-dependent pathways (NrdZ and MutAB) regulated? Moreover, why has CDC1551 retained an intact B12 riboswitch motif upstream of metE despite the loss of metH function? This question, in particular, might inform the observation that only a small proportion (3 of 20) of sequenced vitamin B12-resistant isolates of CDC1551 and H37Rv ΔmetH(B) possessed mutated B12 riboswitch motifs. Through the selective application of the methionine synthase mutants described here, as well as others containing disruptions in B12 biosynthetic pathways, we are actively addressing these issues.

Finally, the disruption of metH in a clinical strain suggests the dispensability of this enzyme for M. tuberculosis pathogenesis. However, the effect that loss of the alternative methionine synthase has on the pathogenesis of M. tuberculosis remains to be determined. The epidemiology of disease caused by strain CDC1551 may be instructive: the strain was originally isolated as the highly infectious agent of a number of tuberculosis outbreaks (21, 22). Is it significant, therefore, that deletion polymorphisms affecting two of the three B12-dependent enzymes (NrdZ and MetH) have been identified in individual M. tuberculosis clinical isolates (7, 19) that, by definition, are in active circulation? That is, does loss of B12-dependent enzymes favor transmission and disease? In this regard, it is intriguing to note that preliminary sequence data from two other clinical isolates, strain C (Mycobacterium tuberculosis Sequencing Project, Broad Institute of Harvard and the Massachusetts Institute of Technology [http://www.broad.mit.edu]) and strain 210 (http://www.tigr.org), have revealed separate sequence polymorphisms in metH. The consequences of these polymorphisms for metH functionality are unknown; however, given that adaptive evolution of M. tuberculosis is dependent entirely on chromosomal rearrangements and mutations, at the very least these observations suggest that the metH locus may be under active selective pressure.

Supplementary Material

[Supplemental material]


This work was supported by grants from the Medical Research Council of South Africa, the National Research Foundation, and the NHLS Trust and by an International Research Scholar's grant from the Howard Hughes Medical Institute (to V.M.).

Preliminary sequence data were obtained from the Broad Institute of Harvard and the Massachusetts Institute of Technology and from the Institute for Genomic Research. We are grateful to Helena Boshoff for the kind gift of M. tuberculosis CDC1551 and for constructively reviewing the manuscript. We also thank Stewart Cole for generously providing the M. tuberculosis H37Rv bacterial artificial chromosome library.


[down-pointing small open triangle]Published ahead of print on 16 February 2007.

Supplemental material for this article may be found at http://jb.asm.org/.


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