The methionine salvage pathway in Bacillus subtilis
© Sekowska and Danchin 2002
Received: 4 March 2002
Accepted: 25 April 2002
Published: 25 April 2002
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© Sekowska and Danchin 2002
Received: 4 March 2002
Accepted: 25 April 2002
Published: 25 April 2002
Polyamine synthesis produces methylthioadenosine, which has to be disposed of. The cell recycles it into methionine through methylthioribose (MTR). Very little was known about MTR recycling for methionine salvage in Bacillus subtilis.
Using in silico genome analysis and transposon mutagenesis in B. subtilis we have experimentally uncovered the major steps of the dioxygen-dependent methionine salvage pathway, which, although similar to that found in Klebsiella pneumoniae, recruited for its implementation some entirely different proteins. The promoters of the genes have been identified by primer extension, and gene expression was analyzed by Northern blotting and lacZ reporter gene expression. Among the most remarkable discoveries in this pathway is the role of an analog of ribulose diphosphate carboxylase (Rubisco, the plant enzyme used in the Calvin cycle which recovers carbon dioxide from the atmosphere) as a major step in MTR recycling.
A complete methionine salvage pathway exists in B. subtilis. This pathway is chemically similar to that in K. pneumoniae, but recruited different proteins to this purpose. In particular, a paralogue or Rubisco, MtnW, is used at one of the steps in the pathway. A major observation is that in the absence of MtnW, MTR becomes extremely toxic to the cell, opening an unexpected target for new antimicrobial drugs. In addition to methionine salvage, this pathway protects B. subtilis against dioxygen produced by its natural biotope, the surface of leaves (phylloplane).
The fate of methylthioribose (MTR), the end-product of spermidine and spermine metabolism, as well as of ethylene biosynthesis has not yet been fully explored in most organisms. In Escherichia coli this molecule is excreted in the medium  while in Klebsiella pneumoniae it constitutes the methionine salvage pathway, being metabolized back into methionine [2, 3]. In eukaryotic parasites it is also recycled into methionine, presumably through a pathway similar to that in K. pneumoniae. In Bacillus subtilis we found that MTR is an excellent sulfur source  and we unraveled some of the steps involved in its metabolism, which starts from phosphorylation of MTR, mediated by the MtnK protein .
It has been shown previously that the ykrW gene, annotated as similar to ribulose phosphate carboxylase/oxygenases (Rubisco) in the original sequence, has links with sulfur metabolism. Indeed, Henkin and co-workers found that the corresponding coding sequence (CDS) was preceded by a S-box typical of sulfur metabolism genes in B. subtilis and Hanson and Tabita found that two classes of enzymes similar to Rubisco were associated with sulfur metabolism . Interestingly, these authors, working with Chlorobium, which uses the reverse TCA cycle for CO2 fixation, postulated these proteins as possible precursors of cyanobacteria, then plant Rubisco at an early time of the development of life on Earth.
This raised interesting questions about the origin of this pathway. In particular the YkrW gene origin could have been early in evolution, or resulting from lateral transfer from plants to bacilli. We demonstrate here that proteins YkrUWXYZ are needed for MTR recycling into methionine in B. subtilis, while YkrV, an aminotransferase, is probably more specific of methionine transamination, but is dispensable in the present conditions because of the present of a variety of izozymes (up to nine amino acid transaminases are present in B. subtilis).
Phenotype of gene inactivation in the mtn region.
Growth on MTR as sole sulfur source
Wild type +O2 a
normal growth after four days
Wild type -O2 a
no growth after four days
mtnS (ykrS) b
no growth (numerous revertants)
weak residual growth
The promoter of mtnV is located 42 nt upstream from the translation start point. Its start lies 8 nt downstream from a putative -10 box identified in the sequence (TATGAT) separated by 17 nt from -35 box (TTTACT) (see Fig. 2.B). The mtnU and mtnV genes share the same promoter region (94 nt) but are transcribed in divergent orientation from overlapping promoters. Thus, the -10 box of the mtnV promoter is situated between the -10 and -35 boxes of the mtnU promoter and the -10 box of the mtnU promoter is situated between the -10 and -35 boxes of the mtnV promoter.
The mtnKS promoter region is 326 nt long. Its start was found to lie 7 nt downstream from a putative -10 box identified in the sequence (TACCAT) (see Fig. 2.C). Upstream from this box and separated by 18 nt is a -35 box (TTGACA), a typical B. subtilis sigmaA-dependent promoter. Downstream of this promoter lies an S-box regulatory sequence.
Genes mntWXYZ are expressed from two overlapping promoters that are situated in a 195 nt long region. The upstream P1 promoter's start was found to lie 7 nt downstream from a putative -10 box identified in the sequence (GATAAT) separated by 17 nt from a consensus -35 box (TTGACA). The P2 promoter's start was found to lie 7 nt downstream from a putative -10 box identified in the sequence (TAAAAT) upstream from which is a -35 box (ATGGGA) (see Fig. 2.D). This promoter region is also reminiscent of regions recognized by the developmental sigmaH transcriptional regulator. The -10 box of the P1's promoter and the -35 box of P2 are partly overlapping. The relative intensity of the signals indicates that transcription from the P1 promoter is more abundant than from P2 (see Fig. 2.D).
When mtnW and mtnZ gene specific probes were used, two bands were revealed: one of about 2.5 kb and second of about 3.2 kb (Fig. 3.B and 3.C)). The larger band corresponds to the expected length of a transcript initiated at the mtnW promoter and terminating in a stem and loop structure at the end of the mtnWXYZ transcriptional unit. The smaller band can possibly be the result of RNA processing at the end of the S-box regulatory sequence of the 5' extremity of the transcript. The intensity of bands when hybridizing RNA from cells grown with sulfate as sulfur source was higher than when using RNA from cells grown in the presence of methionine (lane 1 and 2 in Fig. 3.B and 3.C).
As shown previously, mtnK and mtnS are expressed as an operon, while mtnU is expressed independently .
Expression of mtn::lacZ transcriptional fusions.
β-galactosidase Activity (U mg-1 of protein)a
ED1 medium with sulfate
ED1 medium with methionine
The genes from the mtnWXYZ transcriptional unit (strains BSHP7014, BFS1852, BSHP7016 and BFS1853 for mtnW::lacZ, mtnX::lacZ, mtnY::lacZ and mtnZ::lacZ, respectively) are expressed in a coordinated and sulfur source-dependent way. The expression of the first gene in the operon (mtnW) is higher than that of the last one (mtnZ) with intermediary values for intermediary genes mtnX and mtnY. This suggests the effect of some transcription polarity during the process of transcription (see Table 2). A 5-fold difference is observed between the expression of the mtnWXYZ genes in the presence of sulfate and that in the presence of methionine (579 U/mg of protein in the exponential growth phase in the presence of sulfate and 113 U/mg of protein in the exponential growth phase in the presence of methionine for the mtnW::lacZ transcriptional fusion and 280 U/mg of protein in the exponential growth phase in presence of sulfate and 57 U/mg of protein in the exponential growth phase in presence of methionine for mtnZ::lacZ transcriptional fusion). This observation is in accordance with the presence of S-box regulatory element in the promoter region of mtnWXYZ operon which modulates gene expression as a function of methionine availability .
In order to identify the methionine salvage pathway we made constructs allowing us to decipher the order of the gene products in the pathway, together with in silico, physiologic and genetic analysis of the effect of metabolites of the pathway. This is reminiscent of the way advocated by Koonin et al. for the use of in silico approaches as complement to in vivo experiments .
Since this dioxygenase is coded in the mtn operon we can infer that it indeed displays the corresponding activity , and we therefore renamed it MtnZ. In K. pneumoniae, the immediate precursor activity is that of a coupled phosphatase. The presence of MtnX, which belongs to family pfam00702 comprising phosphatases is strongly suggestive of its involvement at this step . We are thus left with two enzymes, and two steps. We also know, from the genetic data, that the steps are catalyzed in the order MtnY, MtnW. Finally, the reaction needed upstream of MtnZ is active on a molecule phosphorylated in position 1. MtnW is very similar to ribulosephosphate carboxylase oxygenase (Rubisco). It is therefore likely to be active on a ribulose-1-phosphate derivative. Hence MtnY, which is similar to the araD gene product of E. coli (ribulose-5-phosphate epimerase) is most likely to be an epimerase that converts MTR-1-P into 5-thiomethyl-ribulose-1-phosphate, which is the substrate of MtnW. This is strongly supported by the list of similarities found about this gene at the SubtiList database http://genolist.pasteur.fr/Subtilist.
At this stage it is difficult to explicitly identify the activity of MtnW. Even in the case of the paradigmatic Rubisco, with many crystal structures known, the exact mechanism of catalysis is still a matter of controversy. However we can note (as did , at a time when they could not propose a function for the protein) that all the residues involved in catalysis have been conserved, the only residues modified being those involved in the binding of the phosphate at position 5 of ribulose diphosphate. The reaction is that of a dehydratase, but the pathway of the reaction is not yet known. Further work will establish the details of the reaction.
Finally MtnU is also defective for MTR recycling. However, this protein is synthesized at a level much lower that that of the other components of the pathway. We can therefore surmise that it is involved in a regulatory step in the pathway.
Several genes in the vicinity of mtnK have been shown to have significant relationships with sulfur metabolism. In particular, it has been known for some time that genes ykrWXYZ were preceded by an S-box, typical of sulfur mediated regulation . In addition, while analyzing the function of ribulose-1,5-diphosphate carboxylase (Rubisco), Hanson and Tabita discovered a class of highly related enzymes that were involved in sulfur metabolism .
Allowing cells to grow in the presence of the toxic MTR analog 3F-MTR, resistant mutants were found in genes mtnK, mtnW and mtnY. The trifluoromethyl group of 3F-MTR is the toxic group of the molecule and it was expected that inactivation of any gene coding for the steps, including permeation, that led from MTR to methionine (the ultimate methyl donor, since AdoMet is an essential metabolite for the cell) would result in a resistant phenotype. Remarkably, no permease gene was found, suggesting that MTR enter the cells via several entries. In addition, apart from the mtnKS and mtnWXYZ operons no other genes was found, suggesting that all essential steps for recycling are coded for by these genes (or that other steps are coded for by redundant genes). The first step of the metabolic pathway is phosphorylation of MTR. The last step, presumably, is transamination, with mtnV being the preferred transaminase.
Interestingly, the pathway described in this work, although similar to that found by the pioneering work of Abeles and co-workers, uses an enzyme, MtnW, which is extremely similar to Rubisco but not present in K. pneumoniae orK. oxytoca[14, 15]. While most of the genome sequence of this bacterium is known http://wit.integratedgenomics.com/GOLD/ no counterpart of MtnW could be found (data not shown). The corresponding activity exists in K. pneumoniae, but no corresponding gene has yet been isolated. As discovered by Hanson and Tabita, MtnW counterparts constitute a special class (class IV) of Rubisco-like enzymes, which are involved in sulfur metabolism: we can presume that they are all part of the methionine salvage pathway in these organisms . Interestingly, the expected reaction required to metabolize 5-thiomethyl-ribulose-1-phosphate is that of a dehydratase that may use a co-factor as a substrate for the reaction . Rubisco, in the presence of carbon dioxide (resp. dioxygen), acts as a carboxylase (resp. dioxygenase) which cleaves the substrate. In the present case we expect that, instead of cleavage, we have maintenance of a five carbon molecule that is dephosphorylated (by MtnX) and subsequently cleaved by dioxygen in the reaction mediated by MtnZ. The counterpart of this activity in other genomes, including those with a methionine salvage pathway is not known.
As a strong support of this schema, we found counterparts of MtnK and of MtnZ in K. pneumoniae, substantiating the proposed pathway. In this latter organism the counterpart of MtnY is not known, and the corresponding step (opening of the MTR-1-P ring with epimerisation) is not known in any organism yet. MtnY is part of a very wide family of aldolases-epimerases-transketolases and in silico prediction of function alone, at this stage is highly problematic (wrong assignment is frequent for similar functions ), but combination with genetic data make the prediction highly probable . We therefore propose that MtnY be used as a basis for annotation of similar gene products. For example in Xylella fastidiosa, gene XF2209 and in Pseudomonas aeruginosa gene PA1683 probably encodes the cognate activity. Noticeably, a counterpart exists in the Human Genome, where a similar pathway operates.
Two gene products are not directly accounted for in the present schema, MtnU and MtnS. MtnU is expressed at a very low level (ten times lower) as compared to MtnW, and this would hardly fit with the expected stoichiometric enzyme concentration usually found in multistep metabolic pathways. In addition, we found in this work that its synthesis is not submitted to any regulation by the sulfur source. Similarly, MtnS, which is highly similar to an eukaryotic translation initiation factor eIF-2B involved in GTP/GDP exchange is a member typical of a class of GTP-dependent regulators. The presence of two regulator molecules in this pathway indicates that it must have an important role in the cell. B. subtilis is likely to strive on the phylloplane. It is therefore regularly submitted to very high local concentrations of oxygen, and we speculate that this pathway, in addition to providing an excellent means to recycle the energy costly methionine, is used as a means to protect the cell against oxygen.
This work demonstrates that a complete methionine salvage pathway exists in B. subtilis. This pathway is chemically similar to that in K. pneumoniae, but recruited different proteins to this purpose. In particular a paralogue or Rubisco, MtnW, is used at one of the steps in the pathway. A major observation stemming from the present experiments is that in the absence of MtnW MTR becomes extremely toxic to the cell. This sensitivity opens an unexpected target for new antimicrobial drugs, since analogs of 5-methylthio-ribulose1-phosphate might have a strong inhibitory effect on growth on bacteria containing this methionine salvage pathway, including Bacillus anthracis.
Bacterial strains and plasmids used in this study.
Strain or plasmid
Genotype or description
Source or reference
K12 supE hsdΔ5 thi Δ (lac-proAB) F' [traD36 proA+ proB+ lacI q lacZΔM15]
K12 supE44 hsdR17 recA1 endA1 gyrA46 thi relA1 lac- F' [proAB+ lacI q lacZΔM15 Tn10(tetR)]
Functional analysis project a 
Functional analysis project a 
Functional analysis project a
Functional analysis project a
mini-Tn10 delivery vector, SpcR, EryR
cloning vector, CmR, AmpR
cloning vector, CmR, AmpR, pxyl promoter, amyE locus integration
pJM mtnW::lacZ (bla::spc b )
pX pxyl mtnXYZ
Standard procedures were used to transform E. coli and transformants were selected on LB plates containing ampicillin, spectinomycin or ampicillin plus spectinomycin. B. subtilis cells were transformed with plasmid DNA following the two-step protocol described previously . Transformants were selected on LB plates containing erythromycin plus lincomycin or spectinomycin or chloramphenicol.
Plasmid DNA was prepared from E. coli by standard procedures . B. subtilis chromosomal DNA was purified as described by Saunders . Restriction enzymes and T4 DNA ligase were used as specified by manufacturers.
DNA fragments used for cloning experiments were prepared by PCR using PfuTurbo DNA polymerase (Stratagene). Amplified fragments were purified by QIAquick PCR Purification Kit (Qiagen). DNA fragments were purified from a gel using Spin-X columns from Corning Costar by subsequent centrifugation and precipitation.
The mtnXYZ region (nucleotides -31 relative to the mtnX translation start point and ending 3 bp after the stop codon of mtnZ) was amplified by PCR using primers introducing a SpeI cloning site at the 5' end and a BamHI cloning site at the 3' end of the fragment. This fragment was then inserted into the SpeI and BamHI sites of xylose-inductible pX plasmid  producing plasmid pHPP7015. Prior to transformation, this plasmid was linearised at its unique ScaI site. Complete integration of the plasmid was obtained by a double cross-over event at the amyE locus, giving strain BSHP7015.
The DNA downstream from the mtnW gene (nucleotides +41 to +257 relative to the translation start point) was amplified by PCR using primers introducing an EcoRI cloning site at the 5' end and a BamHI cloning site at the 3' end of the fragment, then inserted into the EcoRI and BamHI sites of plasmid pJM783  producing plasmid pHPP7014. To introduce an additional antibiotic resistance gene into plasmid pHPP7014, a SmaI restricted spectinomycin resistance cassette  was inserted into the ScaI restriction site of the bla gene producing plasmid pHPP7014bis. The plasmid in which the mtnW gene was disrupted as well as fused (transcriptional fusion) with the lacZ gene was introduced into the chromosome of BSHP7015 strain by a single cross-over event, giving strain BSHP7014.
For transcriptional fusion of mtnY with the lacZ gene, a DNA segment downstream from the mtnY gene (nucleotides + 57 to + 264 relative to the translation start point) was amplified by PCR using primers introducing an EcoRI cloning site at the 5' end and a BamHI cloning site at the 3' end of the fragment, then inserted into the EcoRI and BamHI sites of plasmid pJM783 producing plasmid pHPP7016. The plasmid in which the mtnY gene was disrupted as well as fused (transcriptional fusion) with the lacZ gene was introduced into the chromosome by a single cross-over event, giving strain BSHP7016.
To construct a mtnV transcriptional fusion with the lacZ gene, a DNA fragment downstream from the mtnV gene (nucleotides + 44 to + 259 relative to the translation start point) was amplified by PCR using primers introducing an EcoRI cloning site at the 5' end and a BamHI cloning site at the 3' end of the fragment, then inserted into the EcoRI and BamHI sites of plasmid pJM783 producing plasmid pHPP7011. The plasmid in which the mtnV gene was disrupted as well as fused (transcriptional fusion) with the lacZ gene was introduced into the chromosome by a single cross-over event, giving strain BSHP7020.
Within the framework of a European Union and Japanese projects for the functional analysis of the genome of B. subtilis, more than 2000 genes have been disrupted by fusion with the lacZ reporter gene (http://locus.jouy.inra.fr/cgi-bin/genmic/madbase/progs/madbase.operl and http://bacillus.genome.ad.jp). The strains from the collection used in this study, constructed by Dr S. Krogh, are listed in Table 3.
A transposon bank was constructed by introduction of the mini-Tn10 delivery vector pIC333  into the B. subtilis 168 strain as described previously . Several thousand independent clones were pooled together and 5 samples of chromosomal DNA were prepared for further use. To obtain 3F-MTR resistant clones, B. subtilis 168 was transformed with chromosomal DNA containing previously prepared transposon banks and clones were selected on LB plates containing spectinomycin. Then, using velvets replicas, clones were transferred onto minimal medium plates containing 3F-MTR at 100 μM concentration and allowed to grow for 24 hrs. The single transposon insertion event was confirmed by back-cross into strain 168 and check for 3F-MTR resistance. To determine the location of the transposon insertion, chromosomal DNA was prepared, followed by subsequent digestion with HindIII, self ligation in E. coli XL1-Blue strain and plasmid sequencing. The primers used for sequencing of transposon insertions were the followings: Tn10 left: 5'GGCCGATTCATTAATGCAGGG3' and Tn10 right: 5'CGATATTCACGGTTTACCCAC3'.
Total RNA was obtained from cells growing on ED1 minimal medium with sulfate or methionine as sulfur source to an OD600 of 0.5 using "High Pure RNA Isolation Kit" from Roche. The RNA concentration was determined by light absorption at 260 nm and 280 nm. 2 μg of RNA were loaded onto 1.2% agarose gel to check the RNA purity and integrity.
RNA molecules were separated on 1% agarose gels and transfered to nylon membranes (Hybond-N, Amersham). Efficiency of transfer was monitored by analysis of ethidium bromide-stained material. Membranes were prehybridized at 50°C for 1 hr in DIG Easy Hyb buffer from Roche. Hybridization was performed under the same conditions with mtnV, mtnW or mtnZ specific probes using a non-radioactive DNA labeling and detection kit "Dig-UTP labeling" from Roche.
Primer extension analysis using reverse transcriptase AMV (Roche) was performed as described by  with two oligonucleotides for each promoter identification. For mtnKS promoter the followings primers were used: 5'ACCAGCGTCTCGGCGCGAAAAAAATGCGCCCC3' and 5'TCACAATGGAATTACGGTCGGTTGCTTTTGG3' (+137 to +169 and +172 to +203 with respect to the translation start point, respectively); for the mtnU promoter the followings primers were used: 5'AGTTCATCAAGATTGGCCAGATCATATCCG3' and 5'CAGGCAGAACAAGAACATCAGCATGTTTGC' (-133 to -103 and -90 to -60 with respect to translation start point, respectively); for the mtnV promoter the followings primers were used: 5'GTTTCATCTCCTCAACAATATGCTCAGGAG' and 5'TCCCAGATTGATAACGTCATGTCCTTCTGC' (-166 to -146 and -114 to -84 with respect to the translation start point, respectively); for the mtnWXYZ promoter the followings primers were used: 5'CGTTTCTCGTCCGAATCTTATCTCTCAGCC' and 5'AGCTGCAAGAATTAGCACCGTGCTTTATAAG' (+43 to +73 and +76 to +107 with respect to the translation start point, respectively). The same primers were used for the generation of sequence ladders. Reaction products were separated on 7% denaturing polyacrylamide gel containing 8 M urea. DNA sequences were determined using Sanger's dideoxy chain-termination method with "Thermo Sequenase radiolabeled terminator cycle sequencing kit" from Amersham Pharmacia Biotech.
B. subtilis cells containing lacZ fusions were assayed for β-galactosidase activity as described previously . Specific activity was expressed in Units per mg protein. The Unit used is equivalent to 0.28 nmols min-1 at 28°C. Protein concentration was determined by Bradford's method using a protein assay Kit (Bio-Rad Laboratories). At least two independent cultures were monitored.
Amylase activity was detected after growth of B. subtilis strains on Tryptose Blood Agar Base (TBAB, Difco) supplemented with 10 g/liter hydrolyzed starch (Sigma). Starch degradation was detected by sublimating iodine onto the plates.
We wish to thank Susan Krogh for the construction of the mtnK, mtnU, mtnX and mtnZ mutants during the Bacillus subtilis functional analysis project, and Sandrine Auger for providing the metI mutant.
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