Mechanism of repression of methionine biosynthesis in Escherichia coli. I. The role of methionine, s-adenosylmethionine, and methionyl-transfer ribonucleic acid in repression

Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity

Multidrug-resistant bacterial pathogens are becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. Bacterial central metabolism is crucial for catabolic processes and provides precursors for anabolic pathways, such as the biosynthesis of essential biomolecules like amino acids or vitamins. However, most essential pathways are not regarded as good targets for antibiotic therapy since their products might be acquired from the environment. This issue raises doubts about the essentiality of such targets during infection. A putative target in bacterial anabolism is the methionine biosynthesis pathway. In contrast to humans, almost all bacteria carry methionine biosynthesis pathways which have often been suggested as putative targets for novel anti-infectives. While the growth of methionine auxotrophic strains can be stimulated by exogenous methionine, the extracellular concentrations required by most bacterial species are unknown. Furthermore, several phenotypic characteristics of methionine auxotrophs are only partly reversed by exogenous methionine. We investigated methionine auxotrophic mutants of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli (all differing in methionine biosynthesis enzymes) and found that each needed concentrations of exogenous methionine far exceeding that reported for human serum (∼30 µM). Accordingly, these methionine auxotrophs showed a reduced ability to proliferate in human serum. Additionally, S. aureus and P. aeruginosa methionine auxotrophs were significantly impaired in their ability to form and maintain biofilms. Altogether, our data show intrinsic defects of methionine auxotrophs. This result suggests that the pathway should be considered for further studies validating the therapeutic potential of inhibitors.IMPORTANCE New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated the nutritional needs of methionine auxotrophs of the pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli We found that each auxotrophic strain retained a growth disadvantage at methionine concentrations mimicking those available in vivo and showed that biofilm biomass was strongly influenced by endogenous methionine biosynthesis. Our experiments suggest that inhibition of the methionine biosynthesis pathway has deleterious effects even in the presence of external methionine. Therefore, additional efforts to validate the effects of methionine biosynthesis inhibitors in vivo are warranted.

Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid

Transcriptional control can be used to program cells to label proteins with noncanonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity. We found that these split proteins could be leveraged to create ligand-dependent MetRS using two approaches. When a pair of MetRS fragments was fused to FKBP12 and the FKBP-rapamycin binding domain (FRB) of mTOR and mutations were introduced that direct substrate specificity toward azidonorleucine (Anl), Anl metabolic labeling was significantly enhanced in growth medium containing rapamycin, which stabilizes the FKBP12-FRB complex. In addition, fusion of MetRS fragments to the termini of the ligand-binding domain of the estrogen receptor yielded proteins whose Anl metabolic labeling was significantly enhanced when 4-hydroxytamoxifen (4-HT) was added to the growth medium. These findings suggest that split MetRS can be fused to a range of ligand-binding proteins to create aaRSs whose metabolic labeling activities depend upon post-translational interactions with ligands.

Genome sequence of Escherichia coli J53, a reference strain for genetic studies

Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. coli K-12 which is resistant to sodium azide. This strain has been widely used as a general recipient strain for various conjugation experiments. Here, we report the genome sequence of E. coli J53 (=KACC 16628).

Upregulation of MetC is essential for D-alanine-independent growth of an alr/dadX-deficient Escherichia coli strain

D-Alanine is a central component of the cell wall in most prokaryotes. D-Alanine synthesis in Escherichia coli is carried out by two different alanine racemases encoded by the alr and dadX genes. Deletion of alr and dadX from the E. coli genome results in a D-alanine auxotrophic phenotype. However, we have observed growth of prototrophic phenotypic revertants during routine culturing of a D-alanine auxotrophic strain. We present a detailed comparison of the proteome and transcriptome profiles of the D-alanine auxotroph and a prototrophic revertant strain. Most noticeably, a general upregulation of genes involved in methionine synthesis in the revertant strain was detected. The appearance of the revertant phenotype was genetically linked to point mutations in the methionine repressor gene (metJ). Our results reveal an alternative metabolic pathway which can supply essential d-alanine for peptidoglycan synthesis of alr- and dadX-deficient E. coli mutants and provide evidence for significant alanine racemase coactivity of the E. coli cystathionine beta-lyase (MetC).

Potential for development of an Escherichia coli-based biosensor for assessing bioavailable methionine: a review

Methionine is an essential amino acid for animals and is typically considered one of the first limiting amino acids in animal feed formulations. Methionine deficiency or excess in animal diets can lead to sub-optimal animal performance and increased environmental pollution, which necessitates its accurate quantification and proper dosage in animal rations. Animal bioassays are the current industry standard to quantify methionine bioavailability. However, animal-based assays are not only time consuming, but expensive and are becoming more scrutinized by governmental regulations. In addition, a variety of artifacts can hinder the variability and time efficacy of these assays. Microbiological assays, which are based on a microbial response to external supplementation of a particular nutrient such as methionine, appear to be attractive potential alternatives to the already established standards. They are rapid and inexpensive in vitro assays which are characterized with relatively accurate and consistent estimation of digestible methionine in feeds and feed ingredients. The current review discusses the potential to develop Escherichia coli-based microbial biosensors for methionine bioavailability quantification. Methionine biosynthesis and regulation pathways are overviewed in relation to genetic manipulation required for the generation of a respective methionine auxotroph that could be practical for a routine bioassay. A prospective utilization of Escherichia coli methionine biosensor would allow for inexpensive and rapid methionine quantification and ultimately enable timely assessment of nutritional profiles of feedstuffs.

Genome-scale gene/reaction essentiality and synthetic lethality analysis

Synthetic lethals are to pairs of non-essential genes whose simultaneous deletion prohibits growth. One can extend the concept of synthetic lethality by considering gene groups of increasing size where only the simultaneous elimination of all genes is lethal, whereas individual gene deletions are not. We developed optimization-based procedures for the exhaustive and targeted enumeration of multi-gene (and by extension multi-reaction) lethals for genome-scale metabolic models. Specifically, these approaches are applied to iAF1260, the latest model of Escherichia coli, leading to the complete identification of all double and triple gene and reaction synthetic lethals as well as the targeted identification of quadruples and some higher-order ones. Graph representations of these synthetic lethals reveal a variety of motifs ranging from hub-like to highly connected subgraphs providing a birds-eye view of the avenues available for redirecting metabolism and uncovering complex patterns of gene utilization and interdependence. The procedure also enables the use of falsely predicted synthetic lethals for metabolic model curation. By analyzing the functional classifications of the genes involved in synthetic lethals, we reveal surprising connections within and across clusters of orthologous group functional classifications.

Isozymes of S-adenosylmethionine synthetase are encoded by tandemly duplicated genes in Escherichia coli

The sole biosynthetic route to S-adenosylmethionine, the primary biological alkylating agent, is catalysed by S-adenosylmethionine synthetase (ATP:L-methionine S-adenosyltransferase). In Escherichia coli and Salmonella typhimurium numerous studies have located a structural gene (metK) for this enzyme at 63 min on the chromosomal map. We have now identified a second structural gene for S-adenosylmethionine synthetase in E. coli by DNA hybridization experiments with metK as the probe; we denote this gene as metX. The metX gene is located adjacent to metK with the gene order speA metK metX speC. The metK and metX genes are separated by approximately 0.8 kb. The metK and the metX genes are oriented convergently as indicated by DNA hybridization experiments using sequences from the 5' and 3' ends of metK. The metK gene product is detected immunochemically only in cells growing in minimal media, whereas the metX gene product is detected immunochemically in cells grown in rich media at all growth phases and in stationary phase in minimal media. Mutants in metK or metX were obtained by insertion of a kanamycin resistance element into the coding region of the cloned metK gene (metK::kan) followed by use of homologous recombination to disrupt the chromosomal metK or metX gene. The metK::kan mutant thus prepared does not grow on minimal media but does grow normally on rich media, while the corresponding metX::kan mutant does not grow on rich media although it grows normally on minimal media. These results indicate that metK expression is essential for growth of E. coli on minimal media and metX expression is essential for growth on rich media. Our results demonstrate that AdoMet synthetase has an essential cellular and/or metabolic function. Furthermore, the growth phenotypes, as well as immunochemical studies, demonstrate that the two genes that encode S-adenosylmethionine synthetase isozymes are differentially regulated. The mutations in metK and metX are highly unstable and readily yield kanamycin-resistant cells in which the chromosomal location of the kanamycin-resistance element has changed.

Role of the metF and metJ genes on the vitamin B12 regulation of methionine gene expression: involvement of N5-methyltetrahydrofolic acid

The repression of MetE synthesis in Escherichia coli by vitamin B12 is known to require the MetH holoenzyme (B12-dependent methyltransferase) and the metF gene product. Experiments using trimethoprim, an inhibitor of dihydrofolate reductase, show that the MetF protein is not directly involved in the repression, but that N5-methyltetrahydrofolic acid (N5-methyl-H4-folate), the product of the MetF enzymatic reaction is required. Since the methyl group from N5-methyl-H4-folate is normally transferred to the MetH holoenzyme to form a methyl-B12 enzyme, the present results suggest that a methyl-B12 enzyme is involved in the vitamin B12 repression of metE expression. Other results argue against the possibility that a methyl-B12 enzyme functions in this repression solely by decreasing the cellular level of homocysteine, which is required for MetR activation of metE expression. Experiments with metJ mutants show that the MetJ protein mediates about 50% of the repression of metE expression by B12 but is totally responsible for the regulation of metF expression by vitamin B12.

Transcriptional start and MetR binding sites on the Escherichia coli metH gene

The 5' upstream region of the Escherichia coli metH gene has been sequenced. Primer extension analysis revealed a transcription start site at 324 bases upstream of the initiator codon. An 8 base sequence homologous to the MetR binding region on the E. coli metE gene is present 217 bp downstream of the transcription start site. Gel retardation experiments showed that purified MetR protein could bind to a 30 base oligonucleotide containing the putative MetR binding region. No "met box" was present which explains the relative lack of regulation of the expression of the metH gene by methionine.

Structure-function studies on Escherichia coli MetR protein, a putative prokaryotic leucine zipper protein

The Escherichia coli metR gene has been sequenced. The sequence predicts a protein of 317 amino acids and a calculated molecular weight of 35,628. This is about 15% larger than the protein from Salmonella typhimurium reported previously [Plamann, L.S. & Stauffer, G.V. (1987) J. Bacteriol. 169, 3932-3937]. The protein is a homodimer and contains a leucine zipper motif characteristic of many eukaryotic DNA-binding proteins. Replacement of two of the leucines in the leucine zipper region of the MetR protein, or substitution of proline for one of the leucines, results in loss of biological activity of the protein. In addition, truncation studies have identified a region on MetR that may be involved in the homocysteine activation of metE expression.

Proofreading in vivo: editing of homocysteine by methionyl-tRNA synthetase in Escherichia coli

Previous in vitro studies have established a pre-transfer proofreading mechanism for editing of homocysteine by bacterial methionyl-, isoleucyl-, and valyl-tRNA synthetases. The unusual feature of the editing is the formation of a distinct compound, homocysteine thiolactone. Now, two-dimensional TLC analysis of 35S-labeled amino acids extracted from cultures of the bacterium Escherichia coli reveals that the thiolactone is also synthesized in vivo. In E. coli, the thiolactone is made from homocysteine in a reaction catalyzed by methionyl-tRNA synthetase. One molecule of homocysteine is edited as thiolactone per 109 molecules of methionine incorporated into protein in vivo. These results not only directly demonstrate that the adenylate proofreading pathway for rejection of misactivated homocysteine operates in vivo in E. coli but, in general, establish the importance of error-editing mechanisms in living cells.

Nucleotide sequence of the metH gene of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2

The Escherichia coli K-12 metH gene, encoding the vitamin B12-dependent homocysteine transmethylase, is located between iclR and lysC in the 91-min region of the chromosome. The metH gene has been sequenced and reveals an open reading frame of 3600 bp encoding a polypeptide of 1200 amino acids (aa) with a calculated Mr of 132 628. The first 414 aa of the deduced polypeptide sequence are 92% identical to the 414 aa deduced from the partially sequenced Salmonella typhimurium LT2 metH gene. In-frame fusions of metH to lacZ were used to confirm the reading frame of the metH gene and to study its regulation. metH was repressed tenfold, presumably indirectly, by L-methionine and the metJ gene product, while vitamin B12 did not induce de novo synthesis of MetH.

Regulation of the Escherichia coli glyA gene by the metR gene product and homocysteine

The methionine component of glyA gene regulation in Escherichia coli K-12 was investigated. The results indicate that the glyA gene is positively controlled by the metR gene product. Activation of glyA by the MetR protein requires homocysteine, an intermediate in methionine biosynthesis. The positive-acting metR regulatory system functions independently of a regulatory system shown previously to control glyA gene expression.

The effect of homocysteine on MetR regulation of metE, metR and metH expression in vitro

An Escherichia coli S-30 DNA directed protein synthesis system was used to study the effect of homocysteine on the in vitro expression of the metE, metH and metR genes. In the presence of purified MetR protein, which is known to regulate the expression of these genes, homocysteine activates metE expression and inhibits both metR and metH expression. These findings support the recent in vivo results of Urbanowski, M.L. and Stauffer, G.V. (1989), J. Bacteriol. 171, 3277-3281.

Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression

Studies by Urbanowski et al. [Urbanowski, M. L., Stauffer, L. T., Plamann, L. S. & Stauffer, G. V. (1987) J. Bacteriol. 169, 1391-1397] have identified a regulatory locus, called metR, required for the expression of the metE and metH genes. We recently purified the MetR protein from Escherichia coli and showed that it could stimulate the in vitro expression of the metE gene and autoregulate its own synthesis. In the present study, the purified MetR protein has been shown to stimulate the in vitro expression of the metH gene. Also, the in vitro synthesized MetE, MetH, and MetR proteins were shown to be biologically active. The transcription start sites for the metE and metR genes have been determined, and DNA footprinting experiments have identified regions in the metE-metR intergenic sequence that are protected by either the MetR or MetJ proteins.

DNA sequence of the metC gene and its flanking regions from Salmonella typhimurium LT2 and homology with the corresponding sequence of Escherichia coli

The DNA sequence of the Salmonella typhimurium metC gene and its flanking regions was determined. The metC gene contains an open reading frame of 1185 nucleotides encoding a polypeptide of 395 amino acids with a predicted molecular weight of 42,874 daltons. S1 nuclease mapping experiments located the transcription start site of the metC gene. The nucleotide sequence and the deduced amino acid sequence for the metC genes of S. typhimurium and Escherichia coli were compared. Although there are 279 nucleotide replacements, most do not change the amino acid sequence. Nucleotide sequence analysis of the flanking regions of the S. typhimurium metC gene shows that there is an open reading frame upstream and an open reading frame downstream of the gene. The existence of the divergently transcribed upstream open reading frame (designated ORF1) was confirmed by the construction of an ORF1-lacZ fusion. The transcription start site of ORF1 was determined by S1 nuclease mapping.

Regulation of methionine synthesis in Escherichia coli: effect of the MetR protein on the expression of the metE and metR genes

A plasmid (pRSE562) containing the metE and metR genes of Escherichia coli was used to study the expression of these genes and the role of the MetR protein in regulating metE expression. DNA sequence analysis of the 236-base-pair region separating these genes showed the presence of seven putative met boxes. When this plasmid was used to transform either wild-type E. coli, metE mutant, or metR mutant, MetE enzyme activity increased 5- to 7-fold over wild-type levels. The metR gene was subcloned from pRSE562, and this plasmid, pMRIII, relieved the methionine auxotrophy of a metR mutant after transformation. The metR gene was also cloned into a vector containing the lambda PL promoter, and the MetR protein was overexpressed and purified to near homogeneity. This protein, when added to an in vitro DNA-dependent protein synthesis system in which the MetE and/or MetR proteins were synthesized, caused a large increase in the expression of the metE gene but a decrease in the expression of the metR gene. The in vitro expression of both genes was inhibited by the MetJ protein and S-adenosylmethionine in the presence or absence of MetR protein. These results provide evidence that the product of the metR gene is a trans-activator of the expression of the metE gene and that the expression of the metR gene is under autogenous regulation and is repressed by the MetJ protein.

Methionine biosynthesis in Enterobacteriaceae: biochemical, regulatory, and evolutionary aspects

The genes coding for the enzymes involved in methionine biosynthesis and regulation are scattered on the Escherichia coli chromosome. All of them have been cloned and most have been sequenced. From the information gathered, one can establish the existence (upstream of the structural genes coding for the biosynthetic genes and the regulatory gene) of "methionine boxes" consisting of two or more repeats of an octanucleotide sequence pattern. The comparison of these sequences allows the extraction of a consensus operator sequence. Mutations in these sequences lead to the constitutivity of the vicinal structural gene. The operator sequence is the target of a DNA-binding protein--the methionine aporepressor--which has been obtained in the pure state, for which S-adenosylmethionine acts as the corepressor. Mutations in the corresponding gene lead to the constitutive expression of all the methionine structural genes. The physicochemical properties of the methionine aporepressor are being investigated.

Nucleotide sequence and fine structural analysis of the Corynebacterium glutamicum hom-thrB operon

The complete nucleotide sequence of the Corynebacterium glutamicum hom-thrB operon has been determined and the structural genes and promoter region mapped. A polypeptide of Mr 46,136 is encoded by hom and a polypeptide of Mr 32,618 is encoded by thrB. Both predicted protein sequences show amino acid sequence homology to their counterparts in Escherichia coli and Bacillus subtilis. The promoter region has been mapped by S1-nuclease and deletion analysis. Located between -88, RNA start site and -219 (smallest deletion clone with complete activity) are sequence elements similar to those found in E. coli and B. subtilis promoters. Although there are no obvious attenuator-like structures in the 5'-untranslated region, there is a dyad-symmetry element, which may act as an operator.

Cloning and characterization of the genes for the two homocysteine transmethylases of Escherichia coli

We have cloned the genes for the two homocysteine transmethylases of Escherichia coli K12. The vitamin B12-independent enzyme is encoded by the metE gene while the metH gene codes for the vitamin B12-requiring enzyme. Overexpression of the gene products and Tn1000 mutagenesis have enabled the metE and metH gene products to be identified as 99 kDa and 130 kDa polypeptides, respectively. The truncated polypeptides generated by Tn1000 insertion were used to determine the direction of transcription of the metE and metH genes. Negative complementation suggests that the MetH enzyme exists as an oligomer. Investigation of the expression of the chromosomal- and plasmid-encoded gene products confirms that metE is subject to negative control by vitamin B12 and methionine, and that metH is under positive control by the cofactor and negative control by methionine. For vitamin B12 and methionine to act as regulatory effectors in metE control, functional metH and metJ genes are required, respectively. The use of stable Tn1000-generated fragments of the metE product as electrophoretic markers for the plasmid-encoded metE gene product demonstrated that the two regulatory proteins involved in negative control of metE are present in excess. Under conditions whereby both forms of negative metE control are non-functional, the metE gene product represented about 90% of the total protein, and cell growth was severely impaired.

A new methionine locus, metR, that encodes a trans-acting protein required for activation of metE and metH in Escherichia coli and Salmonella typhimurium

We isolated an Escherichia coli methionine auxotroph that displays a growth phenotype similar to that of known metF mutants but has elevated levels of 5,10-methylenetetrahydrofolate reductase, the metF gene product. Transduction analysis indicates that the mutant carries normal metE, metH, and metF genes; the phenotype is due to a single mutation, eliminating the possibility that the strain is a metE metH double mutant; and the new mutation is linked to the metE gene by P1 transduction. Plasmids carrying the Salmonella typhimurium metE gene and flanking regions complement the mutation, even when the plasmid-borne metE gene is inactivated. Enzyme assays show that the mutation results in a dramatic decrease in metE gene expression, a moderate decrease in metH gene expression, and a disruption of the metH-mediated vitamin B12 repression of the metE and metF genes. Our evidence suggests that the methionine auxotrophy caused by the new mutation is a result of insufficient production of both the vitamin B12-independent (metE) and vitamin B12-dependent (metH) transmethylase enzymes that are necessary for the synthesis of methionine from homocysteine. We propose that this mutation defines a positive regulatory gene, designated metR, whose product acts in trans to activate the metE and metH genes.

Separate regulatory systems for the repression of metE and btuB by vitamin B12 in Escherichia coli

Synthesis of the btuB-encoded outer membrane receptor for vitamin B12 and the metE-encoded homocysteine methyltransferase is repressed by growth of Escherichia coli in the presence of vitamin B12. The regulation by vitamin B12 of the production of beta-galactosidase in strains carrying btuB-lac or metE-lac operon fusions indicated that repression of both genes operates at the transcriptional level. Selection for expression of these fusions under repressive conditions allowed isolation of second-site mutations in which repressibility by vitamin B12 had been lost. Mutations in metH and metF prevented vitamin B12-dependent regulation of metE, but not that of btuB. Mutations in btuB and other genes involved in uptake of the vitamin eliminated or reduced repression. Mutations in the newly identified gene, btuR, controlled the repressibility of btuB, but had no effect on metE regulation. The btuR gene resides at 27.9 min on the genetic map in the gene order cysB-topA-btuR-trp; it acts in a trans-dominant manner and appears to encode a repressor of btuB transcription.

Cloning and characterization of the metC gene from Salmonella typhimurium LT2

The metC gene of Salmonella typhimurium was cloned into the plasmid vectors pACYC184 and pBR322. Genetic and biochemical experiments indicate that the region controlling metC gene expression is present on the cloned fragments. The location of the metC gene was determined by insertional inactivation with transposons Tn5 and mini-Mu. The gene product was identified in a minicell system as a 49-kDa polypeptide. The direction of transcription and translation was determined by correlating the orientation of mini-Mu insertions within the metC gene with the expression of the lacZ gene contained in mini-Mu.

Location of plasmid-mediated citrate utilization determinant in R27 and incidence in other H incompatibility group plasmids

Citrate utilization (Cit+) is encoded by a specific subgroup of incompatibility HI plasmids, viz., IncHI1 plasmids. Only one IncHI1 plasmid, pRG1271, which originated in a Mexican typhoid outbreak in 1972, did not specify Cit+. All other Cit+ plasmids hybridized to a Cit+ probe, a 2-kilobase BglII fragment derived from the Cit+ transposon Tn3411. The position of the Cit+ determinant was mapped to a 13.5-kilobase ApaI fragment within the prototype IncHI1 plasmid R27. No other functions have been mapped within this region. Citrate utilization mediated by IncHI1 was observed only after a prolonged lag period of approximately 150 h, and certain Escherichia coli strains, e.g., E. coli K-12 J53-1, were not able to utilize citrate specified by the H plasmids. Most E. coli strains harboring the multicopy Cit+ plasmid pOH2, a derivative of pBR322, required only 18 to 24 h to express the Cit+ phenotype, but E. coli J53-1 (pOH2) required at least 72 h for expression.

The metH gene from Salmonella typhimurium LT2: cloning and initial characterization

A 19-kb EcoRI DNA fragment carrying the metH gene of Salmonella typhimurium LT2 was cloned into plasmid vector pACYC184 and propagated in Escherichia coli K-12. The size of the metH gene product was observed to be approx. 120 kDa, as determined by SDS-polyacrylamide gel analysis of plasmid-specific polypeptides synthesized in a minicell system. The direction of transcription of the metH gene relative to the cloned fragment was determined, and the positions of translation initiation and termination were estimated.

Molecular cloning and characterization of the MET6 gene of Saccharomyces cerevisiae

A yeast DNA fragment complementing the met6 mutation in yeast (Saccharomyces cerevisiae) was cloned in a shuttle vector, Yep13, by transforming a yeast host with plasmid DNA prepared from yeast gene bank CV13 of K. Nasmyth. A restriction map of a 6-kb Sau3A insert was constructed. A 2.6-kb fragment (Sau3A-BamHI) complementing the mutation was found by subcloning. Evidence that the DNA fragment contains the yeast MET6 gene was obtained by genomic integration. A 2.5-kb transcript is found both in wild-type (wt) and met6 yeast strains by Northern blotting experiments, indicating that the mutation acts at posttranscriptional level. The rate of transcription for the integrant lies between the values observed for the wt and mutant strains. The functional gene product seems to be involved in negative regulation of transcription of the MET6 gene.

Nucleotide sequence and biochemical characterization of the metJ gene from Salmonella typhimurium LT2

The nucleotide sequence of the Salmonella typhimurium metJ gene is presented along with the sequence of the promoter region for the closely linked metB gene. The two genes are transcribed in opposite directions, with transcription initiating from a single promoter for metB, and from two apparent promoters for metJ. RNA polymerase binding sites for metJ and metB, determined by in vitro protection studies, lie adjacent to each other and may overlap. The two metJ promoters, PJ1 and PJ2, are separated by approximately 65 base pairs. Binding of RNA polymerase in vitro could only be observed for PJ1, even though transcripts are initiated from both promoters in vivo. The metJ gene codes for a polypeptide of 105 amino acids with a calculated Mr of 12,110. The translation start site was determined by N-terminal amino acid sequence analysis of a metJ-lacZ fusion protein.

Cloning and initial characterization of the metJ and metB genes from Salmonella typhimurium LT2

The metJ and metB genes of Salmonella typhimurium have been cloned into Escherichia coli K-12 on a 19-kb EcoRI fragment in the plasmid vector pACYC184. The presence of a functional metB+ gene on this plasmid, designated pGS89, was demonstrated by its ability to complement a metB- E. coli mutant. The presence of a functional metJ+ gene on this plasmid was demonstrated by its ability to repress metC+ gene expression in a metJ- mutant transformed with this plasmid. The metJ gene product was identified in a minicell system as a polypeptide of Mr 12000. This polypeptide was not produced when the metJ gene was inactivated by insertion of a Tn5 element. Transformation of an E. coli metB- mutant with plasmid pGS89 (metB+, metJ+) results in transformants that grow slowly on glucose-minimal medium or glucose-minimal medium supplemented with homocysteine. Methionine addition, however, restores normal growth. This phenotype requires the relA- mutation in the host strain and at least two other plasmid loci, one of which is the metJ+ gene. Transformation of an E. coli metJ- mutant with metJ- derivatives of plasmid pGS89 results in transformants that are unable to grow on either glucose-minimal medium or glucose-minimal medium supplemented with methionine. This phenotype requires the presence of a functional metB+ gene on the plasmid, and is unrelated to the status of the relA gene.

Molecular cloning and primary structure of the Escherichia coli methionyl-tRNA synthetase gene

The intact metG gene was cloned in plasmid pBR322 from an F32 episomal gene library by complementation of a structural mutant, metG83. The Escherichia coli strain transformed with this plasmid (pX1) overproduced methionyl-tRNA synthetase 40-fold. Maxicell analysis showed that three major polypeptides with MrS of 76,000, 37,000, and 29,000 were expressed from pX1. The polypeptide with an Mr of 76,000 was identified as the product of metG on the basis of immunological studies and was indistinguishable from purified methionyl-tRNA synthetase. In addition, DNA-DNA hybridization studies demonstrated that the metG regions were homologous on the E. coli chromosome and on the F32 episome. DNA sequencing of 642 nucleotides was performed. It completes the partial metG sequence already published (D. G. Barker, J. P. Ebel, R. Jakes, and C. J. Bruton, Eur. J. Biochem. 127:449-451, 1982). Examination of the deduced primary structure of methionyl-tRNA synthetase excludes the occurrence of any significant repeated sequences. Finally, mapping of mutation metG83 by complementation experiments strongly suggests that the central part of methionyl-tRNA synthetase is involved in methionine recognition. This observation is discussed in the light of the known three-dimensional crystallographic structure.

Mutations affecting regulation of methionine biosynthetic genes isolated by use of met-lac fusions

Fusions of the lac genes to the promoters of four structural genes in the methionine biosynthetic pathway, metA, metB, metE, and metF, were obtained by the use of the Mu d(Ap lac) bacteriophage. The levels of beta-galactosidase in these strains could be derepressed by growth under methionine-limiting conditions. Furthermore, growth in the presence of vitamin B12 repressed the synthesis of beta-galactosidase in strains containing a fusion of lacZ to the metE promoter, phi(metE'-lacZ+). Mutations affecting the regulation of met-lac fusions were generated by the insertion of Tn5. Tn5 insertions were obtained at the known regulatory loci metJ and metK. Interestingly, a significant amount of methionine adenosyltransferase activity remained in the metK mutant despite the fact that the mutation was generated by an insertion. Several Tn5-induced regulatory mutations were isolated by screening for high-level beta-galactosidase expression in a phi(metE'-lacZ+) strain in the presence of vitamin B12. Tn5 insertions mapping at the btuB (B12 uptake), metH (B12 dependent tetrahydropteroylglutamate methyltransferase), and metF (5,10-methylenetetrahydrofolate reductase) loci were obtained. The isolation of the metH mutant was consistent with previous suggestions that the metH gene product is required for the repression of metE by vitamin B12. The metF::Tn5 insertion was of particular interest since it suggested that a functional metf gene product was also needed for repression of metE by vitamin B12.

Glutamyl-gamma-methyl ester acts as a methionine analogue in Escherichia coli: analogue resistant mutants map at the metJ and metK loci

Escherichia coliK-12 mutants resistant to glutamyl-γ-methyl ester were isolated. A mutation leading to resistance of up to 1·4 mg/ml of the methionine analogue maps at min 63 and is 13% cotransducible withserAindicating an alteration in themetKgene. Another mutation leading to resistance to 3 mg/ml of the analogue and cross-resistance to other amino acid analogues maps at min 87. This mutation, which has the phenotype of MetJ−, is shown to be situated between theglpKandmetBgenes and thus indicates a different gene order from the published one.

Preferential charging of tRNA-Met-f in Escherichia coli K12

The charging of tRNA-Met-f and tRNA-Met-m in vivo and in vitro and initiation of polysomes during methionine limitation were studied in two strains of Escherichia coli K12. In the wild-type strain the distribution of polysomes as well as the kinetic parameters of methionyl-tRNA synthetase indicate preferential acylation of tRNA-Met-f. This preferential charging of tRNAM-et-f does not take place in a mutant strain which is also defective in initiation of polysomes during methionine limitation.

S-adenosyl methionine requiring mutants in Saccharomyces cerevisiae: evidences for the existence of two methionine adenosyl transferases

Mutants requiring S-adenosyl methionine (SAM) for growth have been selected in Saccharomyces cerevisiae. Two classes of mutants have been found. One class corresponds to the simultaneous occurrence of mutations at two unlinked loci SAM1 and SAM2 and presents a strict SAM requirement for growth on any medium. The second class corresponds to special single mutations in the gene SAM2 which lead to a residual growth on minimal medium but to normal growth on SAM supplemented medium or on a complex medium like YPGA not containing any SAM. These genetic data can be taken as an indication that Saccharomyces cerevisiae possesses two isoenzymatic methionine adenosyl transferases (MAT). In addition, SAM1 and SAM2 loci have been identified respectively with the ETH-10 and ETH2 loci previously described. Biochemical evidences corroborate the genetic results. Two MAT activities can be dissociated in a wild type extract (MATI and MATII) by DEAE cellulose chromatography. Mutations at the SAM1 locus lead to the absence or to the modification of MATII whereas mutations at the SAM2 locus lead to the absence or to the modification of MATI. Moreover, some of our results seem to show that MATI and MATII are associated in vivo.

Isolation of a metK mutant with a temperature-sensitive S-adenosylmethionine synthetase

An Escherichia coli metK mutant, designated metK110, was isolated among spontaneous ethionine-resistant organisms selected at 42 degrees C. The S-adenosylmethionine synthetase activity of this mutant was present at lower levels than in the corresponding wild-type strain and was more labile than the wild-type enzyme when heated or dialyzed. A mixture of mutant and wild-type enzyme preparations had an activity equal to the sum of the component activities. These facts strongly suggest that the mutated gene in this strain is the structural gene for this enzyme. Genetic mapping experiments placed the metK110 mutation near or at the site of other known metK mutants (i.e., 63 min), confirming its designation as a metK mutant. A revised gene order has been established for this region, i.e., metC glc speC metK speB serA.

Influence of methionine biosynthesis on serine transhydroxymethylase regulation in Salmonella typhimurium LT2

The enzyme serine transhydroxymethylase (EC 2.1.2.1; L-serine:tetrahydrofolate-5,10-hydroxymethyltransferase) is responsible both for the synthesis of glycine from serine and production of the 5,10-methylenetetrahydrofolate necessary as a methyl donor for methionine synthesis. Two mutants selected for alteration in serine transhydroxymethylase regulation also have phenotypes characteristic of metK (methionine regulatory) mutants, including ethionine, norleucine, and alpha-methylmethionine resistance and reduced levels of S-adenosylmethionine synthetase (EC 2.5.1.6; adenosine 5'-triphosphate:L-methionine S-adenosyltransferase) activity. Because this suggested the existence of a common regulatory component, the regulation of serine transhydroxymethylase was examined in other methionine regulatory mutants (metK and metJ mutants). Normally, serine transhydroxymethylase levels are repressed three- to sixfold in cells grown in the presence of serine, glycine, methionine, adenine, guanine, and thymine. This does not occur in metK and metJ mutants; thus, these mutations do affect the regulation of both serine transhydroxymethylase and the methionine biosynthetic enzymes. Lesions in the metK gene have been reported to reduce S-adenosylmethionine synthetase levels. To determine whether the metK gene actually encodes for S-adenosylmethionine synthetase, a mutant was characterized in which this enzyme has a 26-fold increased apparent Km for methionine. This mutation causes a phenotype associated with metK mutants and is cotransducible with the serA locus at the same frequency as metK lesions. Thus, the affect of metK mutations on the regulation of glycine and methionine synthesis in Salmonella typhimurium appears to be due to either an altered S-adenosylmethionine synthetase or altered S-adenosylmethionine pools.

Identification of a genetic locus affecting chromosome stabiltiy and cellular survival in a dnaB mutant

A mutation has been identified in an Escherichia coli K-12 strain carrying dnaB42. This mutation potentiates both deoxyribonucleic acid degradation and cell death at nonpermissive temperatures. It is located 2 min away from dnaB between malB and metA.

Studies on metabolic role of 5'-Methylthioadenosine in Ochromonas malhamensis and other microorganisms

Several compound containing a thiomethyl group were found to replace vitamin B12 in a protozoan, Ochromonas malhamensis. The order of the effectiveness was as follows: 5'-methylthioadenosine is greater than S-adenosylmethionine is greater than 5-methylthioribose is greater then L-methionine. A similar order was obtained with respect to the permeability of these compounds into the protozoan cells, except for S-adenosylmethionine. 5'-Methylthioadenosine and 5-methylthioribose as well as L-methionine markedly increased the intracellular content of L-methionine. The level of S-adenosylmethionine was also increased by them, but to lesser degree. The thiomethyl group of the compounds was established to be incorporated into S-adenosylmethionine. The metabolic fate of the thiomethyl group of 5'-methylthioadenosine cannot be distinguished from that of L-methionine. A high activity of 5'-methylthioadenosine nucleosidase was detected in the cell-free extracts of the protozoan. These results strongly suggest that 5'-methylthioadenosine would be metabolized to L-methionine would be ocnverted to S-adenosylmethionine. Like L-methionine and vitamin B12, 5'-methylthioadenosine and 5-methylthioribose may play an important role in maintenance of the C-1 pool in Ochromonas malhamensis. Neither 5'-methylthioadenosine nor 5-methylthioribose replaced vitamin B12 in some vitamin B12-requiring bacteria. This result is consistent with the fact that neither compounds was significantly taken up by these bacteria.

Methionine metabolism in BHK cells: selection and characterization of ethionine resistant clones

The selection of clones resistant to methionine antagonists was undertaken on baby hamster Kidney cells grown in a methionine free medium, supplemented with homocystine, folic acid and hydroxo-B12. Clones resistant to 30 mug/ml ethionine were isolated after mutagenesis at an induced mutation frequency of 2.3 X 10(-5). An ethionine resistant clone, ETH 304, was extensively studied. The resistant cells excreted methionine in the culture medium and the intracellular pools of methionine and SAM were two to five times greater in the resistant clone than in the wild type cells. A semidominant ethionine resistant phenotype was observed in hybrids between the wild type and this resistant clone. Measurement of the specific activity of menadione reductase, B12 methyltransferase and ATP: L-methionine S-adenosyl-transferase in crude extracts of the wild type showed a repressive action of methionine on the level of the three enzymes. However, the ethionine resistant clone ETH 304 was not modified in this function. Menadione reductase is feedback-inhibited by SAM in wild type cells. The enzyme of the ethionine resistant clone was significantly less sensitive to SAM. When a comparison of thermal stability was made between the wild type and ethionine resistant clone enzymes, it was found that the thermal stability of the latter was modified. Three other ethionine resistant clones, independantly isolated, were similarly affected in the properties of menadione reductase. These results suggest that the pathway of re-use of S-adenosyl homocysteine, produced during methylation reactions, is highly regulated by methionine and SAM.