The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity.

The murI gene of Escherichia coli was recently identified on the basis of its ability to complement the only mutant requiring D-glutamic acid for growth that had been described to date: strain WM335 of E. coli B/r (P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx, J. Bacteriol. 174:5772-5779, 1992). We report experiments of insertional mutagenesis of the murI gene which demonstrate that this gene is essential for the biosynthesis of D-glutamic acid, one of the specific components of cell wall peptidoglycan. A special strategy was used for the construction of strains with a disrupted copy of murI, because of a limited capability of E. coli strains grown in rich medium to internalize D-glutamic acid. The murI gene product was overproduced and identified as a glutamate racemase activity. UDP-N-acetylmuramoyl-L-alanine (UDP-MurNAc-L-Ala), which is the nucleotide substrate of the D-glutamic-acid-adding enzyme (the murD gene product) catalyzing the subsequent step in the pathway for peptidoglycan synthesis, appears to be an effector of the racemase activity.     

Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan.

The murI gene of Escherichia coli, whose inactivation results in the inability to form colonies in the absence of D-glutamic acid, was identified in the 90-min region of the chromosome. The complementation of an auxotrophic E. coli B/r strain by various DNA sources allowed us to clone a 2.5-kbp EcoRI chromosomal fragment carrying the murI gene into multicopy plasmids. The murI gene corresponds to a previously sequenced open reading frame, ORF1 (J. Brosius, T. J. Dull, D. D. Sleeter, and H. F. Noller. J. Bacteriol. 148:107-127, 1987), located between the btuB gene, encoding the vitamin B12 outer membrane receptor protein, and the rrnB operon, which contains the genes for 16S, 23S, and 5S rRNAs. The murI gene product is predicted to be a protein of 289 amino acids with a molecular weight of 31,500. Attempts to identify its enzymatic activity were unsuccessful. Cells altered in the murI gene accumulate UDP-N-acetylmuramyl-L-alanine to a high level when depleted of D-glutamic acid. Pools of precursors located downstream in the pathway are consequently depleted, and cell lysis finally occurs when the peptidoglycan content is 25% lower than that of normally growing cells.     

Studies on the Metabolism of D-amino acid in Microorganisms

Several strains of bacteria belonging to genus Aerobacter were found to oxidize D-glutamate rapidly, while tbey show feeble oxidative activity toward the L-form even when they were grown in the medium containing DL-glutamate.

The isolation of L-glutamate, a natural amino acid, from its DL-form was achieved by the degradation of D-glutamic acid using one of these strains.

This may be the first observation on a natural amino acid obtained from the racemic one by the metabolic action of the organism.

A new enzyme, D-glutamic acid oxidase, which is responsible for D-glutamate degradation in this organism and differs from Krebs’ D-amino acid oxidase, has been postulated.     

The Escherichia coli Dga (MurI) protein shares biological activity and structural domains with the Pediococcus pentosaceus glutamate racemase.

The Pediococcus pentosaceus glutamate racemase gene product complemented the D-glutamate auxotrophy of Escherichia coli WM335. Amino acid sequence analysis of the two proteins revealed 28% identity, primarily in six clusters scattered throughout the sequence. Further analyses indicated secondary structure similarities between the two proteins. These data support a recent report that the dga (murI) gene product is a glutamate racemase.     

Resolution of DL-Glutamic Acid with Optically Active Neutral Amino Acid Amides

DL-Glutamic acid has been resolved into optically active forms as the diastereoisomeric salt of optically active neutral amino acid amides, and the salt is easily converted to the sodium salt of the active forms. By resolution with L-tyrosinamide and L-leucinamide, sodium L-glutamate was obtained in 65 and 80 per cent yield respectively. Attempts to extend this method to resolution of DL-glutamic acid using L-phenylalaninamide as resolving agent resulted in poor yield of less pure D-glutamic acid.

By the infrared spectroscopy and X-ray diffraction analysis it has been confirmed that the diastereoisomeric salts of L-leucinamide or L-tyrosinamide with L- or D-glutamic acid compose a combined salt structure in solid state, whereas L-phenylalaninamide with L- or D-glutamic acid does not compose a characteristic diastereoisomeric salt but rather the mechanical mixture of L-phenylalaninamide and L- or D-glutamate anion in solid state.

In the previous study¹⁾, it was reported that L-leucinamide forms the characteristic diastereoisomeric salts with racemic N-acyl mono amino acids, most of which are fairly resolved into their antipodes.     

Staphylococcus haemolyticus contains two D-glutamic acid biosynthetic activities, a glutamate racemase and a D-amino acid transaminase.

Two D-glutamic acid biosynthetic activities, glutamate racemase and D-amino acid transaminase, have been described previously for bacteria. To date, no bacterial species has been reported to possess both activities. Genetic complementation studies using Escherichia coli WM335, a D-glutamic acid auxotroph, and cloned chromosomal DNA fragments from Staphylococcus haemolyticus revealed two distinct DNA fragments containing open reading frames which, when present, allowed growth on medium without exogenous D-glutamic acid. Amino acid sequences of the two open reading frames derived from the DNA nucleotide sequences indicated extensive identity with the amino acid sequence of Pediococcus pentosaceous glutamate racemase in one case and with that of the D-amino acid transaminase of Bacillus spp. in the second case. Enzymatic assays of lysates of E. coli WM335 strains containing either the cloned staphylococcal racemase or transminase verified the identities of these activities. Subsequent DNA hybridization experiments indicated that Staphylococcus aureus, in addition to S. haemolyticus, contained homologous chromosomal DNA for each of these genes. These data suggest that S. haemolyticus, and probably S. aureus, contains genes for two D-glutamic acid biosynthetic activities, a glutamate racemase (dga gene) and a D-amino acid transaminase (dat gene).     

Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase

Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.     

The Escherichia coli mutant requiring D-glutamic acid is the result of mutations in two distinct genetic loci.

D-Glutamic acid is an essential component of bacterial cell wall peptidoglycan in both gram-positive and gram-negative bacteria. Very little is known concerning the genetics and biochemistry of D-glutamate production in most bacteria, including Escherichia coli. Evidence is presented in this report for the roles of two distinct genes in E. coli WM335, a strain which is auxotrophic for D-glutamate. The first gene, which restores D-glutamate independence in WM335, was mapped, cloned, and sequenced. This gene, designated dga, is a previously reported open reading frame, located at 89.8 min on the E. coli map. The second gene, gltS, is located at 82 min. gltS encodes a protein that is involved in the transport of D- and L-glutamic acid into E. coli, and the gltS gene of WM335 was found to contain two missense mutations. To construct D-glutamate auxotrophs, it is necessary to transfer sequentially the mutated gltS locus, and then the mutated dga locus into the recipient. The sequences of the mutant forms of both dga and gltS are also presented.     

Regulatory responses to an oral D-glutamate load: formation of D-pyrrolidone carboxylic acid in humans

Previously published studies have shown D-glutamate to be the most potent natural inhibitor of glutathione synthesis known, yet how D-glutamate is handled in humans is unknown. Therefore, we administered an oral D-glutamate load to four healthy volunteers and monitored the plasma D-glutamate concentration and excretion over a 3-h postload period. Compared with time controls, the plasma D-glutamate concentration increased 10-fold in the 1st h and then reached a plateau over the remaining time course. In contrast, plasma D-pyrrolidone carboxylic acid increased progressively throughout the 3-h time course to a level 10-fold higher than the D-glutamate plasma concentration. Excretion of D-glutamate progressively increased despite a constant filtered D-glutamate load rising from only 5 to 95% of the filtered amount. Excretion of D-pyrrolidone carboxylic acid increased with the rise in filtered load without significant reabsorption. The amount of D-pyrrolidone carboxylic acid excreted over the 3-h time course was 10 times the amount excreted as D-glutamate and accounted for almost 20% of the administered D-glutamate. These findings indicate that plasma D-glutamate concentration is tightly regulated through two mechanisms: 1) the transport into cells and metabolic conversion to D-pyrrolidone carboxylic acid and excretion, and 2) the enhancement of D-glutamate clearance by the kidneys.     

An Escherichia coli gene in search of a function: phenotypic effects of the gene recently identified as murI.

Earlier we reported that an open reading frame located at 89.5 min of the Escherichia coli map (ORFI) codes for a protein of unknown function that could be overexpressed and purified to homogeneity (G. Balikó, A. Raukas, I. Boros, and P. Venetianer, Mol. Gen. Genet. 211:326-331, 1988). In the work described here, we attempted to learn the function of this protein by inactivating the chromosomal gene and providing it or its deletion derivatives on temperature-sensitive plasmids. We found that the presence of the functional ORFI gene is essential; cells are not viable at the nonpermissive temperature or when the region coding for the C-terminal 50 amino acids of the protein is deleted. At intermediate temperatures or when the gene is overexpressed, characteristic changes occur in cell morphology, nucleoid separation during cell division, and supercoiling of plasmids. The possible mechanisms of these effects are discussed in view of the fact that Doublet et al. (P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx, J. Bacteriol. 174:5772-5779, 1992) recently identified the ORFI gene as murI, involved in D-glutamic acid biosynthesis.     

Structure of the hydrolyzed product (F-2) released from gamma-polyglutamic acid by gamma-glutamyl hydrolase YwtD of Bacillus subtilis

The structure of the hydrolyzed product (F-2) with a molecular mass of about 2 kDa released from gamma-polyglutamic acid by the gamma-glutamyl hydrolase YwtD of Bacillus subtilis was analyzed. The results showed that F-2 is an optically heterogeneous polymer consisting of D- and L-glutamic acid in an 80:20 ratio with D-glutamic acid on both the N- and C-terminal sides, suggesting that YwtD is an enzyme that cleaves the gamma-glutamyl bond between D- and D-glutamic acid recognizing adjacent L-glutamic acid toward the N-terminal region.     

D-Glutamic acid-induced muscle contraction in the silkworm, Bombyx mori

Agonists for muscle contraction in silkworms were screened by injecting test solutions into the hemolymph of decapitated silkworm larvae. Kainic acid, a glutamate receptor agonist, and D-glutamic acid induced muscle contractions, and D-aspartic acid was partially effective, whereas NMDA and AMPA, representative mammalian glutamate receptor agonists, did not induce contraction. L-Glutamic acid inhibited the kainic acid or D-glutamic acid-induced contraction. Amino acid analysis revealed that 3% of the total glutamic acid in the silkworm hemolymph is D-glutamic acid. These results suggest that d-glutamic acid acts physiologically as an agonist for muscle contraction in silkworms, and that L-glutamic acid functions as an inhibitor.     

Peptidoglycan-polysaccharide complex in the cell wall of the filamentous prochlorophyte Prochlorothrix hollandica.

A peptidoglycan-polysaccharide complex composed of N-acetylglucosamine, N-acetylmuramic acid, muramic acid 6-phosphate, L-alanine, D-alanine, D-glutamic acid, meso-diaminopimelic acid, N-acetylmannosamine, mannose, galactose, glucose, and phosphate was isolated from cell walls of the filamentous prochlorophyte Prochlorothrix hollandica; this complex was similar in chemical composition and structure to that found in cyanobacteria. Peptide patterns of partial acid hydrolysates of the isolated peptidoglycan revealed an A1 gamma structure with direct cross-linkage (m-diaminopimelic acid-D-alanine) of the peptide side chains. The degree of cross-linkage (63%) was found to be in the range of values obtained for gram-positive bacteria and cyanobacteria.     

Chemical structure and biological activity relationship of bacterial cell walls and muramyl peptides

The biological activities of the cell walls of bacteria having different types of peptidoglycans, and those of stereoisomers and analogs of muramyl dipeptide (MDP), of N-acetylglucosaminyl-beta(1-4)-N-acetylmuramyl tetrapeptides having different L- and D-amino acids at the COOH-terminus, and of 6-O-acyl-MDPs were examined to elucidate the relationship between structure and activity. Replacement of the L-alanine residue of MDP with glycine and replacement of the D-isoglutamine residue with L-isoglutamine, L-glutamic acid, and D-isoasparagine, but not with D-glutamic acid, caused a marked decrease in the biological activities of the MDP molecule. Test disaccharide tetrapeptides, irrespective of the configuration of COOH-terminal amino acid, showed strong immunoadjuvant activity and stimulation of macrophages, whereas those having COOH-terminal L-amino acids exhibited greater pyrogenicity, induction of acute joint inflammation, and hemorrhagic necrosis at a primed site than those having COOH-terminal D-amino acids. Introduction of an alpha-branched higher fatty acid to the muramic acid residue resulted in the disappearance of pyrogenicity after i.v. injection, an increase of adjuvanticity, and a loss of dependence on administration vehicles. The lack of the immunopotentiating activity (adjuvanticity) in cell walls from group B-type bacterial species was explained by the combined inhibitory effects of the replacement of the L-alanine residue by glycine and involvement of the alpha-carboxyl group of the D-glutamic acid residue in linking with neighboring peptide subunits.     

Selection of peptide inhibitors against the Pseudomonas aeruginosa MurD cell wall enzyme

The purified Pseudomonas aeruginosa cell wall biosynthesis MurD amide ligase enzyme was used to screen C-7-C and 12 mers peptides from phage display libraries using competitive biopanning approaches with the specific substrates D-glutamate and ATP. From the 60 phage-encoded peptides identified, DNA was sequenced, deduced amino acid sequences aligned and two peptides were synthesized from consensus sequences identified. The UDP-N-acetylmuramyl-L-alanine MurD substrate was synthesized, purified and used to develop a spectrophotometric assay. One peptide synthesized was found to specifically inhibit ATPase activity of MurD. The IC50 value was estimated at 4 microM for the C-7-C MurDp1 peptide. The loop conformation of MurDp1 was shown to be important for the inhibition of the UDP-N-acetylmuramyl-L-alanine:D-glutamate MurD ligase. The linear 12 mers MurD2 peptide has an IC50 value of 15 mM. A conserved amino acid motif was found between MurDp2 and the bacterial glyceraldehyde 3-phosphate dehydrogenase indicating that MurDp2 binds at a protein-protein interacting site. The approach proposed and results obtained suggest that efficient peptide inhibitors as well as protein-protein interaction domains can be identified by phage display.     

Chemical structure of peptidoglycan in Selenomonas ruminantium: cadaverine links covalently to the D-glutamic acid residue of peptidoglycan

The peptidoglycan of Selenomonas ruminantium, a strictly anaerobic bacterium, contains cadaverine (Y. Kamio, Y. Itoh, Y. Terawaki, and T. Kusano, J. Bacteriol. 145:122-128, 1981). This report describes the chemical structure of the peptidoglycan of this bacterium. The [14C]cadaverine-labeled peptidoglycan was degraded with the lytic enzymes prepared from Streptomyces albus G into three small fragments including a major fragment (band A compound). Bank A compound was composed of L-alanine, D-glutamic acid, meso-diaminopimelic acid, D-alanine, and cadaverine in the molar ratio 0.98:1.0:1.0:0.98:0.97. Diaminopimelic acid, L-alanine, and cadaverine were N-terminal residues in band A compound. When the [14C]cadaverine-labeled band A compound was subjected to partial acid hydrolysis, two peptide fragments were obtained. One of them consisted of diaminopimelic acid and D-alanine; diaminopimelic acid was the N-terminal amino acid, and the other fragment was composed of L-alanine, D-glutamic acid, and cadaverine, of which L-alanine and cadaverine were N-terminal. These results lead us to conclude that the primary peptide structure of band A compound is L-alanyl-D-glutamyl-meso-diaminopimelyl-D-alanine and that cadaverine links covalently to the D-glutamic acid residue.     

Cytoplasmic steps of peptidoglycan synthesis in Escherichia coli.

The cellular pool levels of most of the cytoplasmic precursors of peptidoglycan synthesis were determined for normally growing cells of Escherichia coli K-12. In particular, a convenient method for analyzing the uridine nucleotide precursor contents was developed by associating gel filtration and reverse-phase high-pressure liquid chromatography techniques. The enzymatic parameters of the four synthetases which catalyze the stepwise addition of L-alanine, D-glutamic acid, meso-diaminopimelic acid, and D-alanyl-D-alanine to uridine diphosphate-N-acetylmuramic acid were determined. It was noteworthy that the pool levels of L-alanine, D-glutamic acid, meso-diaminopimelic acid, and D-alanyl-D-alanine were much higher than the Km values determined for these substrates, whereas the molar concentrations of the uridine nucleotide precursors were lower than or about the same order of magnitude as the corresponding Km values. Taking into consideration the data obtained, an attempt was made to compare the in vitro activities of the D-glutamic acid, meso-diaminopimelic acid, and D-alanyl-D-alanine adding enzymes with their in vivo functioning, expressed by the amounts of peptidoglycan synthesized. The results also suggested that these adding activities were not in excess in the cell under normal growth conditions, but their amounts appeared adjusted to the requirements of peptidoglycan synthesis. Under the different in vitro conditions considered, only low levels of L-alanine adding activity were observed.     

Effect of various analogues of D-glutamic acid on the D-glutamate-adding enzyme from Escherichis coli

Abstract Twenty-four analogues of D-glutamic acid were tested as substrates or inhibitors of the D-glutamate-adding enzyme from Escherichia coli . The best substrates were, in decreasing order of specific activity, D- erythro -4-methylglutamic acid, D- erythro - methylglutamic acid, DL-homocysteic acid, (±)- trans -1-amino-3-carboxy-cyclopentanecarboxylic acid and (±)- trans -1-amino-3-carboxy-cyclohexanecarboxylic acid. Among the different stereoisomers, only the D- erythro isomers for methylglutamic acids, and the trans isomers for the cyclic analogs, were substrates. Apart from the D- erythro -3 and 4-methylglutamic acids and DL-homocysteic acid, none of the examined compounds significantly inhibited the addition of radioactive D-glutamic acid to UDP-N-acetylmuramyl-L-alanine.     

Primary structure of the peptidoglycan from the unicellular cyanobacterium Synechocystis sp. strain PCC 6714

A peptidoglycan fraction free of non-peptidoglycan components was isolated from the unicellular cyanobacterium Synechocystis sp. strain PCC 6714. Hydrofluoric acid treatment (48%, 0 degrees C, 48 h) cleaved off from the peptidoglycan non-peptidoglycan glucosamine, mannosamine, and mannose. The purified peptidoglycan consists of N-acetyl muramic acid, N-acetyl glucosamine, L-alanine, D-alanine, D-glutamic acid, and meso-diaminopimelic acid in approximately equimolar amounts. At least partial amidation of carboxy groups in the peptide subunits is indicated. Peptide analyses and 2,4-dinitrophenyl studies of partial acid hydrolysates revealed the structure of the Synechocystis sp. strain PCC 6714 peptidoglycan to belong to the A1 gamma type (direct cross-linkage) of peptidoglycan classification. The degree of cross-linkage is about 56% and thus is in the range of that found in gram-positive bacteria. Some of the peptide units are present as tripeptides lacking the carboxy-terminal D-alanine.     

The Binding Mode of Second-Generation Sulfonamide Inhibitors of MurD: Clues for Rational Design of Potent MurD Inhibitors

A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using ¹H/¹³C heteronuclear single quantum correlation. The MurD protein was selectively ¹³C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand–MurD complexes and its influence on ligand–enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors.