The activities in vitro of DD-carboxypeptidase and LD-carboxypeptidase of Gaffkya homari during biosynthesis of peptidoglycan

Mechanical Genomic Studies Reveal the Role of d-Alanine Metabolism in Pseudomonas aeruginosa Cell Stiffness

The mechanical properties of bacteria are important for protecting cells against physical stress. The cell wall is the best-characterized cellular element contributing to bacterial cell mechanics; however, the biochemistry underlying its regulation and assembly is still not completely understood. Using a unique high-throughput biophysical assay, we identified genes coding proteins that modulate cell stiffness in the opportunistic human pathogen Pseudomonas aeruginosa. This approach enabled us to discover proteins with roles in a diverse range of biochemical pathways that influence the stiffness of P. aeruginosa cells. We demonstrate that d-Ala—a component of the peptidoglycan—is tightly regulated in cells and that its accumulation reduces expression of machinery that cross-links this material and decreases cell stiffness. This research demonstrates that there is much to learn about mechanical regulation in bacteria, and these studies revealed new nonessential P. aeruginosa targets that may enhance antibacterial chemotherapies or lead to new approaches.

The stiffness of bacteria prevents cells from bursting due to the large osmotic pressure across the cell wall. Many successful antibiotic chemotherapies target elements that alter mechanical properties of bacteria, and yet a global view of the biochemistry underlying the regulation of bacterial cell stiffness is still emerging. This connection is particularly interesting in opportunistic human pathogens such as Pseudomonas aeruginosa that have a large (80%) proportion of genes of unknown function and low susceptibility to different families of antibiotics, including beta-lactams, aminoglycosides, and quinolones. We used a high-throughput technique to study a library of 5,790 loss-of-function mutants covering ~80% of the nonessential genes and correlated P. aeruginosa individual genes with cell stiffness. We identified 42 genes coding for proteins with diverse functions that, when deleted individually, decreased cell stiffness by >20%. This approach enabled us to construct a “mechanical genome” for P. aeruginosa. d-Alanine dehydrogenase (DadA) is an enzyme that converts d-Ala to pyruvate that was included among the hits; when DadA was deleted, cell stiffness decreased by 18% (using multiple assays to measure mechanics). An increase in the concentration of d-Ala in cells downregulated the expression of genes in peptidoglycan (PG) biosynthesis, including the peptidoglycan-cross-linking transpeptidase genes ponA and dacC. Consistent with this observation, ultraperformance liquid chromatography-mass spectrometry analysis of murein from P. aeruginosa cells revealed that dadA deletion mutants contained PG with reduced cross-linking and altered composition compared to wild-type cells.

Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow

LD-Carboxypeptidases (EC 3.4.17.13) are named for their ability to cleave amide bonds between l- and d-amino acids, which occur naturally in bacterial peptidoglycan. They are specific for the link between meso-diaminopimelic acid and d-alanine and therefore degrade GlcNAc-MurNAc tetrapeptides to the corresponding tripeptides. As only the tripeptides can be reused as peptidoglycan building blocks, ld-carboxypeptidases are thought to play a role in peptidoglycan recycling. Despite the pharmaceutical interest in peptidoglycan biosynthesis, the fold and catalytic type of ld-carboxypeptidases are unknown. Here, we show that a previously uncharacterized open reading frame in Pseudomonas aeruginosa has ld-carboxypeptidase activity and present the crystal structure of this enzyme. The structure shows that the enzyme consists of an N-terminal beta-sheet and a C-terminal beta-barrel domain. At the interface of the two domains, Ser(115) adopts a highly strained conformation in the context of a strand-turn-helix motif that is similar to the "nucleophilic elbow" in alphabeta-hydrolases. Ser(115) is hydrogen-bonded to a histidine residue, which is oriented by a glutamate residue. All three residues, which occur in the order Ser-Glu-His in the amino acid sequence, are strictly conserved in naturally occurring ld-carboxypeptidases and cannot be mutated to alanines without loss of activity. We conclude that ld-carboxypeptidases are serine peptidases with Ser-His-Glu catalytic triads.

Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent

The bacterial acyltransferases of the SxxK superfamily vary enormously in sequence and function, with conservation of particular amino acid groups and all-alpha and alpha/beta folds. They occur as independent entities (free-standing polypeptides) and as modules linked to other polypeptides (protein fusions). They can be classified into three groups. The group I SxxK D,D-acyltransferases are ubiquitous in the bacterial world. They invariably bear the motifs SxxK, SxN(D), and KT(S)G. Anchored in the plasma membrane with the bulk of the polypeptide chain exposed on the outer face of it, they are implicated in the synthesis of wall peptidoglycans of the most frequently encountered (4-->3) type. They are inactivated by penicillin and other beta-lactam antibiotics acting as suicide carbonyl donors in the form of penicillin-binding proteins (PBPs). They are components of a morphogenetic apparatus which, as a whole, controls multiple parameters such as shape and size and allows the bacterial cells to enlarge and duplicate their particular pattern. Class A PBP fusions comprise a glycosyltransferase module fused to an SxxK acyltransferase of class A. Class B PBP fusions comprise a linker, i.e., protein recognition, module fused to an SxxK acyltransferase of class B. They ensure the remodeling of the (4-->3) peptidoglycans in a cell cycle-dependent manner. The free-standing PBPs hydrolyze D,D peptide bonds. The group II SxxK acyltransferases frequently have a partially modified bar code, but the SxxK motif is invariant. They react with penicillin in various ways and illustrate the great plasticity of the catalytic centers. The secreted free-standing PBPs, the serine beta-lactamases, and the penicillin sensors of several penicillin sensory transducers help the D,D-acyltransferases of group I escape penicillin action. The group III SxxK acyltransferases are indistinguishable from the PBP fusion proteins of group I in motifs and membrane topology, but they resist penicillin. They are referred to as Pen(r) protein fusions. Plausible hypotheses are put forward on the roles that the Pen(r) protein fusions, acting as L,D-acyltransferases, may play in the (3-->3) peptidoglycan-synthesizing molecular machines. Shifting the wall peptidoglycan from the (4-->3) type to the (3-->3) type could help Mycobacterium tuberculosis and Mycobacterium leprae survive by making them penicillin resistant.

Biosynthesis of peptidoglycan in Gaffkya homari: on the target(s) of benzylpenicillin

The formation of acceptor for the N epsilon-(D-Ala)-acceptor transpeptidase is an essential feature of nascent peptidoglycan processing. In Gaffkya homari the synthesis of cross-bridges in peptidoglycan includes a variety of penicillin-sensitive enzymes, e.g., transpeptidase, DD-carboxypeptidase, and LD-carboxypeptidase. To determine the primary target, we grew cultures in the presence of the MICs of benzylpenicillin (0.2 microgram/ml), methicillin (10 micrograms/ml), cephalothin (5 micrograms/ml), and cefoxitin (25 micrograms/ml) and examined the monomer-dimer composition of each peptidoglycan by high-performance liquid chromatography after muramidase digestion. From these studies it was recognized that of all the dimers, the synthesis of the predominant cross-bridge, diamidated octapeptide (-Ala-iso-D-Gln-Lys-D-Ala -Ala-iso-D-Gln-Lys-D-Ala), is most sensitive to the action of the beta-lactam at its MIC. The enhanced deamidation of the acceptor tetrapeptide, one of the substrates for the transpeptidase, is correlated with the inhibition of this cross-bridge. For example, at the MIC of benzylpenicillin, the ratio of amidated tetrapeptide to nonamidated tetrapeptide decreased from 2.8 in the control to 1.0 in the treated culture. From these results it would appear that a decrease in preferred acceptor for the transpeptidase results in the inhibition of synthesis of this major cross-bridge. Thus, the metabolism of the amide function of the monomer peptides may represent an additional feature of processing in the assembly of cross-bridged dimers in the peptidoglycan of this organism that is sensitive to the action of beta-lactam.

Modulation of antimicrobial effects of beta-lactams by amino acids in vitro

Glycine as well as 11 and 10, respectively, out of a total of 12 D-amino-acids tested increased the antimicrobial efficacy of imipenem (IMI) and of ampicillin (AMP) using the serosensitive strain E. coli ATCC 8739. D-proline was ineffective in assays with IMI as well as D-proline and D-leucine in assays with AMP. - In contrast, L-amino-acids behaved differently: In assays with IMI, 9 out of 13 isomers were ineffective whereas 3 were antagonistic (L-phenylalanine, L-serine, L-tryptophan). In combination with AMP, however, 10 L-amino acids had an antagonistic effect and 2 (L-leucine, L-methionine) were ineffective. L-alanine was an exception and showed a synergism with both antibiotics which was assumed to have been due to a racemase activity of cells. - Seroresistance of E. coli apparently reduced the synergistic effect of glycine and beta-lactams. - Glycine, alanine and tryptophan lost their typical synergistic or antagonistic effect with AMP when tested as di- or tri-amino-acid compounds. This was not the case with di-L-alanine - It is supposed that the synergistic effect of glycine or of D-amino-acids with beta-lactams can be explained mainly by an inhibition of carboxypeptidases.

In vivo target of benzylpenicillin in Gaffkya homari

It has been established that the DD-carboxypeptidase is the primary in vitro target of benzylpenicillin in Gaffkya homari (W. P. Hammes, Eur. J. Biochem. 70:107-113, 1976). To determine whether this enzyme is also the primary target of benzylpenicillin in vivo, we compared the effects of this beta-lactam, cefmenoxime, cephalothin, and cefoxitin on growth with their acylation of penicillin-binding protein (PBP) 9, the DD-carboxypeptidase. Results of three types of experiments with membrane-walls indicated that PBP 9 is this enzyme and that it is the primary in vitro target of these beta-lactams in the synthesis of sodium dodecyl sulfate (SDS)-insoluble peptidoglycan. First, the acylation of PBP 9 by these beta-lactams paralleled the inhibition of DD-carboxypeptidase and the inhibition of SDS-insoluble peptidoglycan synthesis. Second, the rate of benzylpenicillin release from PBP 9 correlated with the recovery of DD-carboxypeptidase. Third, DD-carboxypeptidase activity was detected in a protein with the same apparent molecular weight as PBP 9 after elution from an SDS-polyacrylamide gel. When intact cells were treated with benzylpenicillin, the minimum growth inhibitory concentration (MGIC) correlated with the concentration of [35S]benzylpenicillin required to acylate PBPs 6 and 9 by 50%. When intact cells were treated with cefmenoxime, cephalothin, or cefoxitin, the MGICs correlated with the concentration of unlabeled beta-lactam required to reduce the subsequent binding of [35S]benzylpenicillin by 50% (ED50) for PBP 6. In contrast, the MGICs of these beta-lactams did not correlate with the ED50s for PBP 9. PBP 9 was not acylated by cefmenoxime or cephalothin at their MGICs, whereas this PBP was fully acylated by cefoxitin at one-tenth of its MGIC. It is suggested that PBP 6 may be a primary target of growth inhibition by benzylpenicillin, cefmenoxime, cephalothin, and cefoxitin; PBP 9, the DD-carboxypeptidase, is dispensable for growth under laboratory conditions; and PBP 9 does not appear to be a primary in vivo target of these beta-lactams, even though this PBP is their primary target in vitro.

LD-carboxypeptidase activity in Escherichia coli. II. Isolation, purification and characterization of the enzyme from E. coli K 12

A LD-carboxypeptidase from Escherichia coli K 12 was isolated by Tris-EDTA treatment and purified to electrophoretic homogeneity by DEAE-cellulose chromatography. The enzyme has a molecular weight of approximately 12,000 as determined by sodium dodecyl sulfate-polyacrylamide electrophoresis and by Sephadex G-100 gel filtration. The studies of the substrate specificity of the enzyme revealed that UDP-MurNAc-tetrapeptide is a superior substrate, with a Km value of 1 X 10(-4) mol/l. The activity of the LD-carboxypeptidase was inhibited by D-amino acids and the beta-lactam antibiotic nocardicin A. Ki values of 0.3 and 43 mmol/l were determined for nocardicin A and D-homoserine, respectively. The properties of the purified enzyme correspond to activity I in ether treated cells.

LD-carboxypeptidase activity in Escherichia coli. I. The LD-carboxypeptidase activity in ether treated cells

The activities of the LD-carboxypeptidases of Escherichia coli K 12 and of a mutant strain 155 with reduced activities were studied with the aid of ether treated cells. Evidence was obtained that was consistent with the suggestion that in both strains two LD-carboxypeptidase activities are present. Activity I degrades the nucleotide activated precursor UDP-MurNAc-tetrapeptide and activity II splits off D-alanine residues from position 4 of the peptide subunits in the nascent murein. In the mutant strain activity I is reduced 10fold compared with strain K 12, whereas activity II is not affected. The two activities could be distinguished with regard to their sensitivity to D-amino acids and the beta-lactam antibiotic thienamycin.

Solid-state 15N NMR studies of the effects of penicillin on cell-wall metabolism of Aerococcus viridans (Gaffkya homari)

Lyophilized whole cells and isolated cell walls from Aerococcus viridans (Gaffkya homari) grown on a synthetic medium containing benzylpenicillin, and either L-[epsilon-15N]lysine or 15N-ammonium ion as the only source of label, have been studied using cross-polarization magic-angle spinning 15N nuclear magnetic resonance. The lysine is incorporated directly into protein and cell-wall peptidoglycan and was used to measure cell-wall cross-links. The ammonium ion acts as a non-specific label monitoring general metabolism. Inhibition of cell-wall cross linking by penicillin occurs, but may not be the exclusive cause of cell death and lysis in this microorganism. Instead, the disruption of the mechanism for control of peptidoglycan synthesis probably is a contributing factor.

Biosynthesis of peptidoglycan in Gaffkya homari: processing of nascent glycan by reactivated membranes

Membranes from Gaffkya homari reactivated by freezing and thawing were used to study the processing events involved in the assembly of both sodium dodecyl sulfate (SDS)-insoluble peptidoglycan (PG) and SDS-soluble PG. The ability to reactivate membranes for the synthesis of these polymers provided an opportunity to monitor those events that are not influenced by wall-linked PG. In G. homari, processing for the formation of cross-links requires the selective actions of DD-carboxypeptidase, LD-carboxypeptidase, and NE-(DAla)-Lys transpeptidase. Time courses of cross-link formation, as measured by the amounts of amidated bisdisaccharide peptide dimer and nonamidated bisdisaccharide peptide dimer, showed a lack of correlation with those for the synthesis of SDS-insoluble PG. SDS-soluble PG, which is significantly cross-linked when synthesized in the absence of penicillin G, was a precursor of the SDS-insoluble PG. In the presence of penicillin G, un-cross-linked SDS-soluble PG was synthesized. This PG was also utilized and processed for the synthesis of cross-linked SDS-insoluble PG after removal of the beta-lactam. This protocol provided a method for separating stages in the synthesis and elongation of PG from those involved in processing. Cross-linkage in the various PG fractions ranged from 0 to 19% in SDS-soluble PG and from 2 to 24% in SDS-insoluble PG. Thus, the results indicated that there is no direct correlation between SDS insolubility and the degree of cross-linkage. Instead, they suggested that additional features may contribute to the insolubility of PG in SDS.

Lipopolymers, isoprenoids, and the assembly of the gram-positive cell wall

Several lines of evidence suggest that Gram-positive bacterial cell surface polymers are synthesized by stepwise addition of polymer subunits to an amphipathic acceptor. In the case of membrane-bound lipopolymers such as mannan and lipoteichoic acid, the finished product may be covalently linked to a lipid anchor. In the case of polymers that are transferred into preexisting cell wall, such as teichoic acid and peptidoglycan, two alternative fates might be possible: (1) transfer into wall with concomitant or later cleavage of the lipid anchor, with recycling of the lipid anchor or secretion of the lipid anchor into the growth medium, and (2) transfer into wall without cleavage of the lipid anchor, resulting in maintenance of the covalent relationship between lipid anchor and polymer chain. In the latter case, a close relationship should be established between the cell wall and the plasma membrane. A number of Gram-positive bacteria have been shown to be resistant to plasmolysis. Therefore, a model for the assembly of the Gram-positive cell wall is proposed which takes into account a role for lipopolymeric intermediates and which views the establishment of resistance to plasmolysis as the natural consequence of such a mechanism.

Biosynthesis of peptidoglycan in Gaffkya homari: reactivation of membranes by freeze-thawing in the presence and absence of walls

The reactivation of membranes from Gaffkya homari for the synthesis of sodium dodecyl sulfate-insoluble peptidoglycan (SDS-insoluble PG) was achieved by successive cycles of freeze-thawing (- 196 versus 25 degrees C). The presence of G. homari walls during this process affected the synthesis of both SDS-soluble (nascent) and SDS-insoluble PG. At two cycles the synthesis of SDS-soluble PG decreased by 70%, whereas that of SDS-insoluble PG increased sevenfold when compared with membranes reactivated in the absence of walls but assayed in the presence of walls. Moreover, at six cycles the lag time for the synthesis of SDS-insoluble PG decreased from 15 min to 5 to 7 min. Walls from G. homari could not be replaced with walls from Bacillus megaterium or cellulose. In addition to these effects, the presence of walls from G. homari or B. megaterium or of cellulose during the incubation of membranes freeze-thawed in the absence of walls increased twofold the amount of SDS-insoluble PG. Reactivated membranes showed greater sensitivities to penicillin (an inhibitor of dd-carboxypeptidase) and d-methionine (an inhibitor of ld-carboxypeptidase) than did isolated membrane-walls. The percentage of cross-linking of the SDS-insoluble PG synthesized by the reactivated system was 34%, a value similar to that observed for the polymer synthesized by isolated membrane-walls. Freeze-thawing membranes and walls together gave a complex with a density different from that of either membranes or walls. Thus, the assembly system for the synthesis and processing of PG was reconstituted in a complex of membranes and walls prepared from the isolated components. Whether this complex has the exact interrelationship between membrane and wall found in the organism has not been established.

Membrane-wall interrelationship in Gaffkya homari: sulfhydryl sensitivity and heat lability of nascent peptidoglycan incorporation into walls

Membrane-walls from Gaffkya homari require a specific interrelationship between membrane and wall that functions in the incorporation of nascent peptidoglycan into the preexisting peptidoglycan of the wall. Two different methods were used to inhibit selectively this incorporation process: (i) sensitivity to sulfhydryl reagents and (ii) heat inactivation. Of the sulfhydryl reagents tested, 2.2 mM iodoacetamide inhibited the synthesis of wall peptidoglycan 50%, whereas greater than 100 mM was required to inhibit the synthesis of sodium dodecyl sulfate (SDS)-soluble peptidoglycan. Heat treatment at 37 degrees C (t 1/2 = 5.7 min) inhibited wall peptidoglycan synthesis without affecting SDS-soluble peptidoglycan synthesis. Inhibition of LD-carboxypeptidase by iodoacetamide and heat gave 50% inhibition and t 1/2 values similar to those observed for the incorporation process. Thus, it is suggested that the LD-carboxypeptidase may be one of the enzymes responsible for the sulfhydryl sensitivity and heat lability and that this enzyme may play a role in the relationship between membrane and wall in G. homari.

The LD-carboxypeptidase activity in Gaffkya homari. The target of the action of D-amino acids or glycine on the formation of wall-bound peptidoglycan

The effects in vitro of D-amino acids or glycine on the formation of wall-bound peptidoglycan were studied with wall membrane enzyme preparations from Gaffkya homari. These amino acids inhibited the incorporation of nascent peptidoglycan into the preformed polymer (e.g. ID50 values for D-alanine, D-leucine, and glycine = 5.6 mmol/l, 1.3 mmol/l, and 11 mmol/l, respectively). The inhibition was accompanied by an incorporation of the inhibitor into position 4 of the peptide subunit Ala1-DGlu2(Lys3-DAla4), where the indices refer to the position of an amino acid residue within the peptide subunit. It is suggested that the reaction is catalyzed by an LD-carboxypeptidase. Therefore, this enzyme has also D-amino acid exchange activity. At inhibitory concentration fewer tripeptide subunits were formed in the nascent peptidoglycan in favour of the formation of tetrapeptide subunits bearing the inhibitor at the C termini. The tripeptide subunits are assumed to be necessary in order that nascent peptidoglycan is utilized as substrate in the transpeptidation reaction. Thus an essential role of the LD-carboxypeptidase is indicated.