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Journal of Bacteriology, January 1999, p. 662-665, Vol. 181, No. 2
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
S-Methylmethionine Metabolism in
Escherichia coli
Martin
Thanbichler,
Bernhard
Neuhierl, and
August
Böck*
Lehrstuhl für Mikrobiologie der
Universität München, D-80638 Munich, Germany
Received 6 August 1998/Accepted 6 November 1998
 |
ABSTRACT |
Selenium-accumulating Astragalus spp. contain an enzyme
which specifically transfers a methyl group from
S-methylmethionine to the selenol of selenocysteine, thus
converting it to a nontoxic, since nonproteinogenic, amino acid.
Analysis of the amino acid sequence of this enzyme revealed that
Escherichia coli possesses a protein (YagD) which shares
high sequence similarity with the enzyme. The properties and
physiological role of YagD were investigated. YagD is an
S-methylmethionine: homocysteine methyltransferase which
also accepts selenohomocysteine as a substrate. Mutants in
yagD which also possess defects in metE and
metH are unable to utilize S-methylmethionine
for growth, whereas a metE metH double mutant still grows
on S-methylmethionine. Upstream of yagD and
overlapping with its reading frame is a gene (ykfD) which, when inactivated, also blocks growth on methylmethionine in a metE metH genetic background. Since it displays sequence
similarities with amino acid permeases it appears to be the transporter
for S-methylmethionine. Methionine but not
S-methylmethionine in the medium reduces the amount of
yagD protein. This and the existence of four MET box motifs
upstream of yfkD indicate that the two genes are members of
the methionine regulon. The physiological roles of the ykfD
and yagD products appear to reside in the acquisition of
S-methylmethionine, which is an abundant plant product, and its utilization for methionine biosynthesis.
 |
TEXT |
Escherichia coli is known
to possess two enzymes (methionine synthases) that catalyze the last
step in methionine biosynthesis. The metE gene product, a
zinc-containing monomer (9) with a molecular mass of 85 kDa
(37), transfers the methyl group of N5-methyl-tetrahydrofolate to the thiolate of
homocysteine. The second enzyme, the metH gene product, is
also a monomer but with a size of 136 kDa (8); it catalyzes
methyl transfer from N5-methyl-tetrahydrofolate to the
cob(I)alamine coenzyme and from there to homocysteine. MetH exhibits a
distinct structure of four domains, which can be correlated with the
partial reactions catalyzed: an N-terminal homocysteine binding domain
carrying a zinc ion, an N5-methyl-tetrahydrofolate binding
domain, a cobalamine binding domain, and a C-terminal domain for
S-adenosylmethionine binding involved in reactivation of the
oxidized cob(II)alamine form (6, 10, 11). Since E. coli cannot synthesize corrinoids, MetH is only active when
cobalamine is present in the medium. MetH is about 100-fold more active
than MetE, which is, however, compensated by the very strong expression
of the metE gene (37).
Cloning and sequencing of the gene for a selenocysteine
methyltransferase (smtA) from Astragalus
bisulcatus involved in selenium tolerance and comparison of the
sequence with entries in the databases revealed that E. coli
possesses a gene (yagD) whose derived product shares 40%
amino acid sequence identity with SmtA (25). In addition, YagD shows low sequence similarities to the amino-terminal domain of
MetH and to human betaine:homocysteine methyltransferase (data not
shown). The regions that are conserved among these proteins comprise
the GGCC motif containing Cys310 and Cys311 and the GLNCA motif around
Cys247 (numbering refers to MetH from E. coli). These cysteine residues were identified as putative ligands of the zinc cofactor of MetH (10, 26). In accordance with this, human betaine:homocysteine methyltransferase was shown to also contain zinc,
which presumably is ligated by cysteine residues (24). These
findings indicate that YagD may be a zinc-dependent methyltransferase which uses a catalytical mechanism similar to that of MetH (10, 26). The YagD protein was purified and shown to synthesize
methionine from S-methylmethionine or
S-adenosylmethionine and homocysteine (25), an
activity previously described for crude extracts from this organism
(2) and for enriched protein preparations of Saccharomyces cerevisiae (31, 32) and
Canavalia ensiformis (1). Formally, therefore,
YagD constitutes a third methionine synthase in E. coli. In
this communication we report on its physiological role in the sulfur
metabolism of this organism.
Physiological role of the homocysteine methyltransferase.
To
elucidate the role of the YagD protein in methionine metabolism, a
mutant was constructed with an in-frame deletion in both the
metE and metH genes. For this purpose,
chromosomal copies of the two genes were amplified by PCR. After
deletion of residues 493 to 1665 of metE and residues 1198 to 1554 of metH, the mutant genes were re-introduced into
wild-type strain KL19 (20) by homologous recombination
according to the method of Hamilton et al. (13). Stationary
cells (see Fig. 1) of the resulting strain, MTD23, were then used to
inoculate minimal medium containing 15 µM (each) different
supplements to an optical density at 600 nm (OD600) of
0.05. Throughout this work M9 minimal medium (30) containing
0.8% glucose and the supplement indicated was used. L-S-methylmethionine was from Acros Organics (Geel,
Belgium). All other compounds were purchased from Sigma (Deisenhofen,
Germany). After 18 h of aerobic incubation at 37°C, the cell
densities of the cultures were measured. The OD600 values
(± standard deviations) obtained were 0.056 (± 0.003) without any
supplement, 0.280 (± 0.002) with DL-methionine sulfoxide,
0.380 (± 0.006) with L-methionine, 0.074 (± 0.002) with
S-adenosyl-L-methionine, 0.771 (± 0.001) with
DL-S-methylmethionine, and 0.679 (± 0.005) with
L-S-methylmethionine. These results demonstrate
that L-methionine, DL-methionine sulfoxide, and
S-methylmethionine complement auxotrophy of the strain. YagD does not contribute to the utilization of methionine sulfoxide, because
no transfer of the methyl group of this compound to homocysteine takes
place (data not shown). Presumably, methionine sulfoxide is converted
to methionine via reduction (7). The lower OD value obtained
for this substrate may be due to its slower utilization in comparison
to methionine (7, 12). With
S-adenosyl-L-methionine (AdoMet), only marginal
growth could be observed, which probably resulted from utilization of
impurities contained in the AdoMet preparation. This finding is in
accordance with previous observations, namely that E. coli
K-12 and its derivatives are largely impermeable to AdoMet
(14). Growth yield with the L form of
S-methylmethionine and the racemate was about twice that
obtained with L-methionine.
The YagD homocysteine methyltransferase does not utilize the
D stereoisomer of S-methylmethionine as a
substrate (25). It was, therefore, surprising that the
DL racemate yielded the same cell mass as the L
form. This result was supported in an experiment in which a series of
different concentrations of
DL-S-methylmethionine and
L-methionine were supplemented (Fig.
1). The data indicate that
D-methylmethionine is converted to the L form
prior to its utilization, possibly via the same pathway as the
conversion of D-methionine to L-methionine
(5).

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FIG. 1.
Effects of yagD and ykfD
mutations on the utilization of S-methylmethionine. Cells of
strains MTD23 ( metE metH), MTD123 ( yagD
metE metH), and MTD234 ( metE metH ykfD)
were grown in minimal medium containing 100 µM
L-methionine. After 18 h of aerobic incubation at
37°C, they were washed, resuspended in 0.9% NaCl to an
OD600 of 10, and transferred into minimal medium containing
different concentrations of L-methionine (met) or
DL-S-methylmethionine (methyl-met),
respectively. The initial OD600 was 0.05. After 18 h
of aerobic incubation at 37°C, the resulting cell densities were
determined. The data shown represent the mean values of at least two
independent growth experiments.
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|
To assess the involvement of the
yagD gene product in
S-methylmethionine metabolism, an in-frame deletion
(residues 270 to
548) was introduced into the corresponding gene of
strain MTD23
according to the method of Hamilton et al.
(
13), yielding the
triple mutant MTD123 (
yagD
metE
metH). An immunoblotting analysis
using antiserum
directed against homocysteine methyltransferase
confirmed that there
was no cross-reacting material (data not
shown). The results of the
growth experiment shown in Fig.
1 prove
that metabolism of
S-methylmethionine requires a functional YagD
protein, since
inactivation of the
yagD gene abolishes the capacity
to grow
on
S-methylmethionine.
ykfD, a gene coding for a putative
S-methylmethionine permease.
The results described
above point to a role for the YagD homocysteine methyltransferase in
the utilization of external S-methylmethionine as a source
for methionine. Since there is no evidence in the literature that
E. coli is able to synthesize S-methylmethionine, there might be a transport system for its uptake from the medium. The
results presented previously do not exclude that
S-methylmethionine uses the methionine uptake system
(16, 17).
An inspection of the genomic sequence of
E. coli in the
vicinity of
yagD revealed that upstream of
yagD
there is an open reading
frame of 1,533 bp (
ykfD) coding for
a putative protein and overlapping
with the
yagD reading
frame by 14 bp (
4) (Fig.
2).
Its amino
acid sequence shares significant sequence similarity with
that
of amino acid permeases (data not shown). This similarity and
the
overlapping reading frames might be an indication that
ykfD codes for a
S-methylmethionine transporter which is
cotranscribed
with the
yagD gene.

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FIG. 2.
Chromosomal organization of the ykfD and
yagD open reading frames. The restriction sites used in this
study are shown. Putative MET boxes in the 5' region of ykfD
are depicted as boxed nucleotide sequences. The degrees of identity
with the MET box consensus sequence 5'-AGACGTCT-3' are
indicated. Possible translational start codons are marked by boldface
letters.
|
|
To test this assumption we introduced an in-frame deletion into
ykfD (residues 304 to 1089) and combined this mutation with
the
metE metH lesions of strain MTD23 according to the
method
of Hamilton et al. (
13). The resulting triple mutant,
MTD234
(
metE
metH
ykfD), was tested for growth on
different supplements.
Figure
1 demonstrates that the
ykfD
lesion prevents growth on
S-methylmethionine but not on
methionine. The control strain MTD23,
in contrast, is able to utilize
S-methylmethionine. Immunoblotting
analysis of cell lysates
from strain MTD234 grown in minimal medium
supplemented with 20 µM
L-methionine confirmed that the
yagD gene
was
expressed (data not shown). Thus, the mutation in
ykfD did
not abolish YagD formation by any polarity effect. At
S-methylmethionine
concentrations of higher than 50 µM
slow but significant growth
of strain MTD234 could be observed, which
may indicate nonspecific
transport of the compound via other systems
(data not
shown).
Regulation.
The phenotypes of the ykfD and
yagD mutants described above indicate a physiological role
for the gene products in the acquisition of external
S-methylmethionine and in its conversion into methionine. This could imply that the two genes are subject to regulation by the
MetJ-S-adenosyl-methionine system. MetJ is a homodimer of
12-kDa promoters (35, 36). It binds to the MET box
(5'-AGACGTCT-3') in the upstream region of genes
(metA, metBL, metC, metF,
metJ, metR, and metE) whose products
are involved in methionine biosynthesis and acts as a transcriptional
repressor (3, 18, 28, 29). Between two and five of these MET
boxes are organized in tandem repeats. Because of cooperative
interactions between the repressor molecules bound, their number and
match with the consensus sequence determines the level of
repressibility. S-adenosylmethionine, which is synthesized
from methionine and adenosine triphosphate by the metK gene
product (21), acts as a corepressor (27, 33, 34)
and thereby mediates methionine regulation of the met regulon.
Upstream of
yagD, no sequence similar to that of the MET box
motif can be found. In contrast, there are four of these motifs
upstream of
ykfD (Fig.
2). Depending on which of the two ATG
codons
of the
ykfD gene is functioning for the start of the
translation,
the four MET boxes overlap or immediately precede the
start of
the reading
frame.
To analyze whether the
ykfD yagD putative transcriptional
unit is indeed under control of methionine, cultures of
E. coli KL19 (wild type) were grown in minimal medium supplemented
with
different concentrations of
L-methionine or
DL-
S-methylmethionine.
After 230 min of growth,
cells were harvested and analyzed for
the formation of YagD protein by
immunoblotting (Fig.
3). It is
evident
that the amount of YagD protein was strongly reduced when
40 µM
L-methionine or higher concentrations were present in the
medium. Supplementation of
S-methylmethionine only caused a
slight
reduction in the amount of YagD, which might be due to its
intracellular
conversion into methionine. Similar results were obtained
when
synthesis of YagD was followed by measuring enzyme activity
(results
not shown).

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FIG. 3.
Influence of methionine and
S-methylmethionine supplementation on the expression of
yagD. Minimal medium containing different concentrations of
L-methionine (A) or
DL-S-methylmethionine (B) was inoculated to an
OD600 of 0.05 with stationary cells (see legend to Fig. 1;
grown without L-methionine) of wild-type strain E. coli KL19. After 230 min of aerobic incubation at 37°C, the
cells were harvested and lysed. The proteins were separated on a 15%
polyacrylamide gel in the presence of sodium dodecyl sulfate
(19). The detection of YagD was performed by immunoblotting
analysis using anti-YagD antiserum (obtained from Eurogentech, Belgium,
by custom immunization of a rabbit with purified YagD) in a 1:4,000
dilution, protein A-horseradish peroxidase conjugate (Bio-Rad, Munich,
Germany), and chemiluminscence blotting substrate from Boehringer
(Mannheim, Germany).
|
|
The results described here identify the function of two unassigned open
reading frames from
E. coli. Their products are involved
in
the uptake of
S-methylmethionine and in the methyl transfer
to homocysteine, rendering two molecules of methionine. Such an
activity has been described for crude extracts from
E. coli
cells
by Balish and Shapiro (
2).
S-methylmethionine is a compound
synthesized and stored by
many plant species (
15,
23), and
expression of
ykfD and
yagD enables
E. coli to
utilize this compound.
The abilities of other methionine auxotrophic
bacterial species
to use
S-methylmethionine as a source of
methionine (
22) might
be based on similar systems. In
agreement with this physiological
role,
ykfD and
yagD are subject to control of expression by methionine,
thus constituting two more genes belonging to the methionine regulon.
More detailed studies, however, are required to confirm that MetJ
is
involved as a regulatory protein. On the basis of the results
obtained
in this study we propose the new gene designation
mmu (
S-methylmethionine utilization). Accordingly, the gene
coding
for the putative
S-methylmethionine permease
(
ykfD) is renamed
mmuP, and the
S-methylmethionine:homocysteine methyltransferase
gene
(
yagD) is renamed
mmuM.
 |
ACKNOWLEDGMENTS |
We thank Valerie Maples and Sidney R. Kushner for providing the
sequence of pMAK700.
This work was supported by grants from the Deutsche
Forschungsgemeinschaft and the Fonds der Chemischen Industrie.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Institute of
Genetics and Microbiology, Maria-Ward-Strasse 1a, D-80638 Munich,
Germany. Phone: 89-17919856. Fax: 89-17919863. E-mail:
august.boeck{at}lrz.uni-muenchen.de.
 |
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Journal of Bacteriology, January 1999, p. 662-665, Vol. 181, No. 2
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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Hondorp, E. R., Matthews, R. G.
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