D-alanine oxidase form Escherichia coli: localization and induction by L-alanine

Dialyzed membranes of Escherichia coli prepared by an ethylenediaminetetraacetic acid-lysozyme method catalyze the oxidation of both l-alanine and d-alanine. The specific activities for the oxidations of both d-alanine and l-alanine are increased fivefold when the cells are grown in the presence of either l-alanine or dl-alanine, but are increased only slightly when grown in the presence of d-alanine. In the dl-alanine-induced system, the specific activities for the oxidations of some other d-amino acids are also raised. dl-alanine also induces two other alanine catabolizing enzymes, alanine dehydrogenase and alanine-glutamate aminotransferase which are found in the "soluble" fraction of lysozyme-treated cells. The oxidations of both l-alanine and d-alanine were associated with the membranes of induced cells. After the membranes were disintegrated by sonic treatment, both l-alanine and d-alanine oxidation catalysts sedimented in a sucrose density gradient together with d-lactate and l-lactate dehydrogenases, apparently as a single multienzyme complex.     

Studies on Escherichia coli enzymes involved in the synthesis of uridine diphosphate-N-acetyl-muramyl-pentapeptide

The specific activities of l-alanine:d-alanine racemase, d-alanine:d-alanine ligase, and the l-alanine, d-glutamic acid, meso-diaminopimelic acid, and d-alanyl-d-alanine adding enzymes were followed during growth of Escherichia coli. The specific activities were nearly independent of the growth phase. d-Alanine:d-alanine ligase was inhibited by d-alanyl-d-alanine, d-cycloserine, glycine, and glycyl-glycine. l-Alanine:d-alanine racemase was found to be sensitive to d-cycloserine, glycine, and glycyl-glycine. The l-alanine adding enzyme was inhibited by glycine and glycyl-glycine.     

Industrial biotransformations for the production of d-amino acids

Optically pure d-amino acids are industrially manufactured by biotransformations of cheap starting materials produced by chemical synthesis or fermentation in combination with the development of enzyme catalysts suitable for the starting materials. dl-Alaninamide, an intermediate of the chemical synthesis of dl-alanine, was efficiently converted to d-alanine by stereoselective hydrolysis with a d-isomer specific amidohydrolase produced by Arthrobacter sp. NJ-26. The total utilization system of dl-alaninamide for the production of optically pure d- and l-alanine was constructed by stereospecific amidohydrolases. On the other hand, d-amino acids were also produced from corresponding l-isomers, which are efficiently manufactured by fermentation. d-Glutamic acid was produced from l-glutamic acid. l-Glutamate was converted to the dl-form by the recombinant glutamate racemase of Lactobacillus brevis ATCC8287. Then l-glutamate in a racemic mixture was selectively decarboxylated to γ-aminobutyrate by the l-glutamate decarboxylase of E. coli ATCC11246. As a result of successive enzymatic reactions, d-glutamate was efficiently produced from l-glutamate by a one-pot reaction. d-Proline was produced by the same strategy from l-proline using the recombinant proline racemase of Clostridium sticklandii ATCC12262. In this case, l-proline was degraded by Candida sp. PRD-234. The strategy from l-amino acids to d-amino acids could be applicable to the manufacture of many d-amino acids.     

The relation of d-alanine and alanine racemase activity in molluscs

• 1.1. Eighteen molluscan species were examined for the presence of d-alanine and alanine racemase activity to probe the probable relation between them.
• 2.2. Two bivalve species had high concentration of d-alanine and l-alanine (1:1) and showed high activities of alanine racemase. In these species, the occurrence of d-alanine could be explained by the action of alanine racemase.
• 3.3. In other species, the levels of d-alanine and enzyme activity were low, and the occurrence of d-alanine did not correspond with the presence of alanine racemase activity.
• 4.4. The mechanism of the occurrence of d-alanine in molluscan tissues seems to vary from species to species and seems not to be associated with the phylogenic situation or habitats of the respective species.

     

Mechanism of D-cycloserine action: transport systems for D-alanine, D-cycloserine, L-alanine, and glycine

The accumulation of d-alanine, l-alanine, glycine, and d-cycloserine in Escherichia coli was found to be mediated by at least two transport systems. The systems for d-alanine and glycine are related, and are separate from that involved in the accumulation of l-alanine. d-Cycloserine appears to be primarily transported by the d-alanine-glycine system. The accumulation of d-alanine, glycine, and d-cycloserine was characterized by two line segments in the Lineweaver-Burk analysis, whereas the accumulation of l-alanine was characterized by a single line segment. d-Cycloserine was an effective inhibitor of glycine and d-alanine accumulation, and l-cycloserine was an effective inhibitor of l-alanine transport. The systems were further differentiated by effects of azide, enhancement under various growth conditions, and additional inhibitor studies. Since the primary access of d-cycloserine in E. coli is via the d-alanine-glycine system, glycine might be expected to be a better antagonist of d-cycloserine inhibition than l-alanine. Glycine and d-alanine at 10(-5)m antagonized the effect of d-cycloserine in E. coli, whereas this concentration of l-alanine had no effect.     

Structural specificity of synthetic peptide adjuvant for induction of experimental allergic encephalomyelitis

The peptide N-acetylmuramyl-l-alanyl-d-isoglutamine (MDP), which has adjuvant activities, and 17 of its derivatives and analogs were synthesized and assayed to elucidate the structure necessary for adjuvant activity in induction of experimental allergic encephalomyelitis (EAE) in guinea pigs. The results revealed the importance of the d configuration and the α-carboxamide group of the isoglutaminyl residue of MDP for adjuvant activity. Replacement of the l-alanyl residue of MDP by d-alanine, but not by l-serine or glycine, resulted in a marked decrease in the activity. The β-methyl glycoside of MDP was found to be more active than the α-methyl derivative. 6-O-Stearoyl-N-acetylmuramyl-l-alanyl-d-isoglutamme showed activity.     

The alanine racemase of Mycobacterium smegmatis is essential for growth in the absence of D-alanine

Alanine racemase, encoded by the gene alr, is an important enzyme in the synthesis of d-alanine for peptidoglycan biosynthesis. Strains of Mycobacterium smegmatis with a deletion mutation of the alr gene were found to require d-alanine for growth in both rich and minimal media. This indicates that alanine racemase is the only source of d-alanine for cell wall biosynthesis in M. smegmatis and confirms alanine racemase as a viable target gene for antimycobacterial drug development.     

Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase

The temperature-sensitive Escherichia coli mutant strain ST-640 lyses at the restrictive temperature except when an osmotic stabilizer or a high concentration of d-alanine is present. The presence of dl-alanyl-dl-alanine does not prevent lysis. The rate of murein synthesis, followed in a wall medium, is decreased at both 30 and 42 C. d-Alanyl-d-alanine and uridine diphosphate-N-acetyl-muramyl (UDP-MurNAc)-pentapeptide are synthesized in decreased amounts, accompanied by accumulation of UDP-MurNAc-tripeptide at 42 C but not at 30 C. Uridine nucleotide precursors leak into the medium, especially out of the mutant cells. This leakage is prevented when NaCl is present. The d-alanine: d-alanine ligase (ADP) (EC 6.3.2.4) of the mutant strain, assayed in crude extracts, is temperature sensitive. The impaired ligase is relatively resistant to d-cycloserine and other inhibitors of the enzyme. Combined genetic and enzymatic results show that the low ligase activity is due to a mutation in the ddl gene, the structural gene for d-alanine: d-alanine ligase.     

Characterization of the Alanine Racemases from <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> PAO1

Alanine racemases are ubiquitous, almost uniquely prokaryotic enzymes catalyzing the racemization between l- and d-alanine. The requirement for d-alanine as a necessary component of the bacterial cell wall makes this class of enzymes a logical target for the development of novel antibiotics. In an effort to better understand the structure and mechanism of these enzymes, we have cloned the two independent alanine racemases from Pseudomonas aeruginosa, an important opportunistic bacterial pathogen of humans and animals. The dadX(PA) and alr(PA) genes have been sequenced, overexpressed, and their activity was demonstrated by complementing d-alanine auxotrophs of Escherichia coli. Both gene products were purified to electrophoretic homogeneity, the enzymes were characterized biochemically, and preliminary crystals were obtained.     

Occurrence of d-alanine in the eggs and the developing embryo of the sea urchin Paracentrotus lividus

• 1.1. d-Alanine has been found in appreciable amounts in the eggs and embryos of the sea urchin Paracentrotus lividus.
• 2.2. The content of d-alanine, expressed as pmol/egg or embryo, is 1.32 in the egg, 0.81 in the blastula, 0.54 in the gastrula and 0.60 in the pluteus.
• 3.3. The percentage of d-alanine with respect to the total alanine (d + l) decreases during embryonic development.
• 4.4. d-Amino acid oxidase, d-alanine transaminase and d-alanine racemase activities were found neither in eggs nor in embryos.
• 5.5. Therefore, it does not appear likely that d-alanine is subject to oxidative metabolism.
• 6.6. The decrease in this d-amino acid during development may be due to its utilization in the synthesis of a more complex molecule.

     

d-Alanine as a biomarker and a therapeutic option for severe influenza virus infection and COVID-19

Since the outbreak of coronavirus disease 2019 (COVID-19), biomarkers for evaluating severity, as well as supportive care to improve clinical course, remain insufficient. We explored the potential of d-amino acids, rare enantiomers of amino acids, as biomarkers for assessing disease severity and as protective nutrients against severe viral infections. In mice infected with influenza A virus (IAV) and in patients with severe COVID-19 requiring artificial ventilation or extracorporeal membrane oxygenation, blood levels of d-amino acids, including d-alanine, were reduced significantly compared with those of uninfected mice or healthy controls. In mice models of IAV infection or COVID-19, supplementation with d-alanine alleviated severity of clinical course, and mice with sustained blood levels of d-alanine showed favorable prognoses. In severe viral infections, blood levels of d-amino acids, including d-alanine, decrease, and supplementation with d-alanine improves prognosis. d-Alanine has great potentials as a biomarker and a therapeutic option for severe viral infections.     

D-alanine oxidase from Escherichia coli: participation in the oxidation of L-alanine

Cell wall-membrane preparations of Escherichia coli, prepared by the ethylenediaminetetraacetic acid-lysozyme method, contain enzymes which catalyze the oxidation of d-alanine and, to a lesser extent, l-alanine into pyruvate and ammonia without the formation of hydrogen peroxide. The kinetic parameters were (i) pH optima of 8.3 to 8.4 for l- and d-alanine and (ii) a K(m) value of 6.6 +/- 0.2 mM for d-alanine. Several coenzymes were without effect when added to the reaction mixture. The participation of d-alanine oxidase in the oxidation of l-alanine was demonstrated. The evidence is based on (i) results of cellular fractionation; (ii) labeling experiments; (iii) inhibition studies with aminooxyacetate and cycloserine; (iv) denaturation experiments; and (v) demonstration of the presence of an active racemase.     

Regulation of leucine catabolism in Pseudomonas putida

The generation time of Pseudomonas putida with l-leucine was 20 h in synthetic media but only 3 h with d-leucine. Slow growth in the presence of l-leucine was partially overcome by addition of 0.1 mM amounts of either d-valine, l-valine, or 2-ketoisovalerate. The activities of five enzymes which take part in the oxidation of leucine by P. putida were measured under various conditions of growth. Four enzymes were induced by growth with dl-leucine as sole source of carbon: d-amino acid dehydrogenase, branched-chain keto acid dehydrogenase, 3-methylcrotonyl-coenzyme A carboxylase, and 3-hydroxy-3-methylglutaryl-coenzyme A lyase. The segment of the pathway required for oxidation of 3-methylcrotonate was induced by growth on isovalerate or 3-methylcrotonate without formation of the preceding enzymes. The synthesis of carboxylase and lyase appeared to have been repressed by the addition of l-glutamate or glucose to cells growing on dl-leucine as the sole carbon source. Mutants unable to grow at the expense of isovalerate had reduced levels of carboxylase and lyase, whereas the levels of three enzymes common to the catabolism of all three branched-chain amino acids and those of two isoleucine catabolic enzymes were normal.     

Modification of an effector strain for replacement therapy of dental caries to enable clinical safety trials

AIMS: To construct a genetically modified strain of Streptococcus mutans for dental caries prevention. The strain has significantly reduced cariogenicity owing to a deletion of the entire open reading frame for lactate dehydrogenase, and has excellent colonization potential through the production of a natural antibiotic called mutacin 1140. For use in human clinical trials, additional mutations were introduced to enable rapid elimination of the strain in case of adverse side effects and to increase genetic stability. METHODS: Deletion mutations were introduced into the dal gene for d-alanine biosynthesis and the comE gene for genetic transformation. The resulting strain, A2JM, was tested for dependence on exogenous d-alanine and its ability to be eradicated from colonized rats. The strain was also tested for its ability to exchange DNA with another strain of S. mutans in in vitro and in vivo models. CONCLUSIONS: A2JM was completely dependent on exogenous d-alanine, but could colonize the oral cavity of rats in low numbers in the absence of dietary d-alanine. Results indicated that A2JM can scavenge d-alanine from other plaque bacteria. Lowering of the total oral bacterial load through daily application of chlorhexidine enabled virtually complete eradication of A2JM. The introduction of the comE gene did not significantly decrease the transformability of A2JM in in vitro or in vivo models. The addition of a deletion in the comE gene does, nonetheless, provide additional safety as it has a very low reversion frequency. SIGNIFICANCE AND IMPACT OF THE STUDY: Based on the safety and efficacy profiles established in vitro and in animal models, A2JM appears suitable for safe use in human clinical trials.     

Amino acid compostion of walls from single and filamentous cells of Clostridium acidiurici

Gaffar, Abdul (Brigham Young University, Provo, Utah), David R. Terry, and Richard D. Sagers. Amino acid composition of walls from single and filamentous cells of Clostridium acidiurici. J. Bacteriol. 91:1618-1624. 1966.-The walls from single and filamentous cells of Clostridium acidiurici were shown to contain 11 amino acids: aspartic acid, serine, glutamic acid, proline, d-alanine, glycine, valine, methionine, valine, leucine, phenylalanine, and lysine. In the walls from cells grown at 37 C, d-alanine was the amino acid present in largest quantity, but in the walls from cells grown at 44 C there was a 50% reduction in the d-alanine content while the levels of the other amino acids were unchanged. Filamentous cells grown at 44 C, then brought to 37 C and transferred to fresh medium, fragmented into short cells within 30 min. Alanine racemase activity was the same in extracts from cells grown at both 37 and 44 C, suggesting that this enzyme was not the major controlling factor in the low content of d-alanine in filaments grown at 44 C. Spent medium from cultures grown at 44 C contained a significant amount of d-alanine, whereas there was no evidence of this amino acid in the spent medium from cultures grown at 37 C.     

The synthesis of peptidoglycan in an autolysin-deficient mutant of Bacillus licheniformis N.C.T.C. 6346 and the effect of β-lactam antibiotics, bacitracin and vancomycin

The synthesis of peptidoglycan by cell-free membrane and membrane+wall preparations from an autolysin-deficient, beta-lactamase-negative mutant of Bacillus licheniformis N.C.T.C. 6346 was studied. The membrane preparation synthesized un-cross-linked polymer, the formation of which was not inhibited by beta-lactam antibiotics. Release of d-alanine by the action of d-alanine carboxypeptidase was inhibited variably according to the antibiotic. This inhibition was reversed by neutral hydroxylamine but not by the action of beta-lactamases or by washing. Bacitracin inhibited peptidoglycan synthesis, but not the d-alanine carboxypeptidase. Examination of peptidoglycan synthesized in the presence of excess of bacitracin showed that synthesis was not restricted to the addition of one disaccharide-pentapeptide unit at each synthetic site, an average of 2-3 disaccharide-pentapeptide units being added. Peptidoglycan synthesis was three- to four-fold more sensitive to vancomycin than was the release of d-alanine by the action of the carboxypeptidase. Incorporation of newly synthesized peptidoglycan into pre-existing cell wall was studied in membrane+wall preparations. This incorporation was catalysed by a benzylpenicillin- and cephaloridine-sensitive transpeptidase. The concentrations of these antibiotics giving 50% inhibition of incorporation were almost identical with those required to inhibit growth of the bacillus. Inhibition of the transpeptidase was reversed by treatment with beta-lactamase or by washing.     

Active transport of D-alanine and related amino acids by whole cells of Bacillus subtilis

Whole cells of Bacillus subtilis transported d-alanine and l-alanine by two different systems. The high-affinity system (K(m) of 1 muM and V(max) of 0.6 to 0.8 nmol/min per mg of protein) was specific for the two stereoisomers of alanine. The low-affinity system (K(m) of 10 muM for l-alanine and 20 muM for d-alanine and glycine) had a V(max) of 5 to 12 nmol/min per mg of protein. This system transported glycine, d-cycloserine, and d-serine, in addition to d- and l-alanine. Azide inhibited the uptake of these amino acids and caused the efflux of d-alanine from preloaded cells. These data suggest that transport of these amino acids is energized by the electron transport chain.     

pH and kinetic isotope effects in d-amino acid oxidase catalysis.

The effects of pH, solvent isotope, and primary isotope replacement on substrate dehydrogenation by Rhodotorula gracilis d-amino acid oxidase were investigated. The rate constant for enzyme-FAD reduction by d-alanine increases approximately fourfold with pH, reflecting apparent pKa values of approximately 6 and approximately 8, and reaches plateaus at high and low pH. Such profiles are observed in all presteady-state and steady-state kinetic experiments, using both d-alanine and d-asparagine as substrates, and are inconsistent with the operation of a base essential to catalysis. A solvent deuterium isotope effect of 3.1 +/- 1.1 is observed on the reaction with d-alanine at pH 6; it decreases to 1.2 +/- 0.2 at pH 10. The primary substrate isotope effect on the reduction rate with [2-D]d-alanine is 9.1 +/- 1.5 at low and 2.3 +/- 0.3 at high pH. At pH 6.0, the solvent isotope effect is 2.9 +/- 0.8 with [2-D]d-alanine, and the primary isotope effect is 8.4 +/- 2.4 in D2O. Thus, primary and solvent kinetic isotope effects (KIEs) are independent of the presence of the other isotope, i.e. the 'double' kinetic isotope effect is the product of the individual KIEs, consistent with a transition state in which rupture of the two bonds of the substrate to hydrogen is concerted. These results support a hydride transfer mechanism for the dehydrogenation reaction in d-amino acid oxidase and argue against the occurrence of any intermediates in the process. A pKa,app of approximately 8 is interpreted to arise from the microscopic ionization of the substrate amino acid alpha-amino group, but also includes contributions from kinetic parameters.     

The characterisation of inducible dehydrogenases specific for the oxidation of d-alanine,allohydroxy-d-proline,choline and sarcosine as peripheral membrane proteins in Pseudomonas aeruginosa

The interaction with the cytoplasmic membrane of the inducible, membrane-bound, cytochrome-linked dehydrogenases specific for the oxidation of d-alanine, allohydroxy-d-proline, choline and sarcosine in Pseudomonas aeruginosa was investigated. The susceptibility of d-alanine dehydrogenase to solubilisation by cation depletion or by washing with high ionic strength buffers indicated that it was a peripheral membrane protein. The effect of various divalent cations in reducing the amount of enzyme released by cation depletion suggests a requirement for Mg²⁺ in the binding of d-alanine dehydrogenase to the cytoplasmic membrane. The peripheral nature of all four dehydrogenases was confirmed by examination of the molecular properties and phospholipid content of preparations of the enzymes solubilised with 1 M phosphate buffer (pH 7.0). Additional confirmatory evidence was provided by Arrhenius plots of membrane-bound activity of d-alanine and allohydroxy-d-proline dehydrogenases which were monophasic and independent of the discontinuities attributable to membrane lipid phase separations which characterise such plots of the activity of integral membrane-bound enzymes. The shape of the Arrhenius plots obtained for the activities of known integral respiratory proteins of P. aeruginosa suggests that these enzymes may remain in a fluid environment throughout the course of the phase separation.     

Proliferation and function of microbodies in the nematophagous fungus Arthrobotrys oligospora during growth on oleic acid or d-alanine as the sole carbon source

Abstract The nematophagous fungus Arthrobotrys oligospora is able to grow on oleic acid or d-alanine as the sole carbon source. During growth on oleic acid, activities of enzymes of the β-oxidation pathway, but not catalase, were induced. In the presence of d-alanine, both d-amino acid oxidase and catalase activities were enhanced. Biochemically and cytochemically, the activities of the above enzymes were assigned to microbodies. The significance of these results in relation to the function of microbodies in trophic hyphae, which are formed during nematode infection, is discussed.