Genetic basis for activity differences between vancomycin and glycolipid derivatives of vancomycin.

Small molecules that affect specific protein functions can be valuable tools for dissecting complex cellular processes. Peptidoglycan synthesis and degradation is a process in bacteria that involves multiple enzymes under strict temporal and spatial regulation. We used a set of small molecules that inhibit the transglycosylation step of peptidoglycan synthesis to discover genes that help to regulate this process. We identified a gene responsible for the susceptibility of Escherichia coli cells to killing by glycolipid derivatives of vancomycin, thus establishing a genetic basis for activity differences between these compounds and vancomycin.

Domain structure analysis of elongation factor-3 from Saccharomyces cerevisiae by limited proteolysis and differential scanning calorimetry.

Elongation-factor-3 (EF-3) is an essential factor of the fungal protein synthesis machinery. In this communication the structure of EF-3 from Saccharomyces cerevisiae is characterized by differential scanning calorimetry (DSC), ultracentrifugation, and limited tryptic digestion. DSC shows a major transition at a relatively low temperature of 39 degrees C, and a minor transition at 58 degrees C. Ultracentrifugation shows that EF-3 is a monomer; thus, these transitions could not reflect the unfolding or dissociation of a multimeric structure. EF-3 forms small aggregates, however, when incubated at room temperature for an extended period of time. Limited proteolysis of EF-3 with trypsin produced the first cleavage at the N-side of Gln775, generating a 90-kDa N-terminal fragment and a 33-kDa C-terminal fragment. The N-terminal fragment slowly undergoes further digestion generating two major bands, one at approximately 75 kDa and the other at approximately 55 kDa. The latter was unusually resistant to further tryptic digestion. The 33-kDa C-terminal fragment was highly sensitive to tryptic digestion. A 30-min tryptic digest showed that the N-terminal 60% of EF-3 was relatively inaccessible to trypsin, whereas the C-terminal 40% was readily digested. These results suggest a tight structure of the N-terminus, which may give rise to the 58 degrees C transition, and a loose structure of the C-terminus, giving rise to the 39 degrees C transition. Three potentially functional domains of the protein were relatively resistant to proteolysis: the supposed S5-homologous domain (Lys102-Ile368), the N-terminal ATP-binding cassette (Gly463-Lys622), and the aminoacyl-tRNA-synthase homologous domain (Glu820-Gly865). Both the basal and ribosome-stimulated ATPase activities were inactivated by trypsin, but the ribosome-stimulated activity was inactivated faster.

Inhibition of transglycosylation involved in bacterial peptidoglycan synthesis.

The continuing spectre of resistance to antimicrobial agents has driven a sustained search for new agents that possess activity on drug resistant bacteria. Although several paths are available to reach this goal, the most generalized would be the discovery and clinical development of an agent that acts on a new target which has not yet experienced selective pressure in the clinical setting. Such a target should be essential to the growth and survival of bacteria, and sufficiently different from, or better still non-existent in, the human host. The transglycosylation reaction that polymerizes biochemical intermediates into peptidoglycan qualifies as such a target. This biochemical system accepts the basic unit N-acetylglucosamine-beta-1, 4-N-acetyl-muramyl-pentapeptide-pyrophosphoryl-undecaprenol (lipid II), and leads to polymerization of the N-acetylglucosamine -beta-1, 4-N-acetyl-muramyl-pentapeptide segment into peptidoglycan. Approaches to targeting this reaction include modification of known glycolipid and glycopeptide natural product antibiotics. The synthesis and antibacterial activity of synthetic analogs of moenomycin having novel antibacterial activities not present in the parent structure will be presented, together with the combinatorial chemistry and assay systems leading to their discovery. Likewise, we will discuss chemical modifications to specific glycopeptide antibiotics that have extended their spectrum to include vancomycin resistant enterococci that substitute D-alanyl-D-lactate for D-alanyl-D-alanine in their peptidoglycan. Two differing theories, one positing the generation of high affinity, specific binding to D-alanyl-D-lactate via glycopeptide dimerization and/or membrane anchoring, and the other supporting direct targeting of the modified glycopeptide to the transglycosylation complex, seek to explain the mechanism of action on vancomycin resistant enterococci. Biochemical evidence in support of these two theories will be discussed.

Targeting cell wall synthesis and assembly in microbes: similarities and contrasts between bacteria and fungi.

icrobial cells possess a form of exoskeleton called the cell wall that protects the organism from osmotic pressure and environmental insults. Synthesis of the various building blocks that make up the cell wall occurs in the cytoplasm, and thus microbial cells face specific biochemical and biophysical problems related to the polymerization, transport, and assembly of building blocks into the final wall structure at an extra-cellular site. Cell walls must also be metabolically and structurally pliable in order to allow for processes such as repair, secretion, DNA exchange, and cell division. In some cases, bacteria and fungi use similar mechanisms, to accomplish synthesis and assembly, while in other cases each used divergent strategies to accomplish specific functions. This review will summarize recent advances in our understanding of fungal and bacterial cell wall synthesis and assembly. We will compare specific pathways used by both fungi and bacteria, paying particular attention to identifying those areas where what is known in one system may point to approaches to solving unanswered questions in the other. The structure, chemical properties, and mechanism of action of select natural and synthetic products which inhibit synthesis or assembly of cells walls will be discussed in terms of similarities in the structures, and/or steps in the synthetic process targeted. In addition, new targets in the pathways will be presented along with recent approaches to the discovery and design of novel inhibitors.

In situ assay for identifying inhibitors of bacterial transglycosylase.

An in situ transglycosylase assay has been developed using endogenously synthesized lipid II. The assay involves the preferential synthesis and accumulation of lipid II in a reaction mixture containing the cell wall membrane material isolated from Escherichia coli, exogenously supplied UDP-MurNAc-pentapeptide, and radiolabeled UDP-GlcNAc. In the presence of Triton X-100, the radiolabeled product formed is almost exclusively lipid II, while the subsequent formation of peptidoglycan is inhibited. Removal of the detergent resulted in the synthesis of peptidoglycan (25% incorporation of radiolabeled material) from the accumulated lipid II. This reaction was inhibited by moenomycin, a known transglycosylase inhibitor. In addition, tunicamycin, which affects an earlier step of the pathway by inhibiting MraY, had no effect on the formation of peptidoglycan in this assay, as expected. Similarly, ampicillin and bacitracin did not inhibit the formation of peptidoglycan under the conditions established.

Chlorobiphenyl-desleucyl-vancomycin inhibits the transglycosylation process required for peptidoglycan synthesis in bacteria in the absence of dipeptide binding.

Novel glycopeptide analogs are known that have activity on vancomycin resistant enterococci despite the fact that the primary site for drug interaction, D-ala-D-ala, is replaced with D-ala-D-lactate. The mechanism of action of these compounds may involve dimerization and/or membrane binding, thus enhancing interaction with D-ala-D-lactate, or a direct interaction with the transglycosylase enzymes involved in peptidoglycan polymerization. We evaluated the ability of vancomycin (V), desleucyl-vancomycin (desleucyl-V), chlorobiphenyl-vancomycin (CBP-V), and chlorobiphenyl-desleucyl-vancomycin (CBP-desleucyl-V) to inhibit (a) peptidoglycan synthesis in vitro using UDP-muramyl-pentapeptide and UDP-muramyl-tetrapeptide substrates and (b) growth and peptidoglycan synthesis in vancomycin resistant enterococci. Compared to V or CBP-V, CBP-desleucyl-V retained equivalent potency in these assays, whereas desleucyl-V was inactive. In addition, CBP-desleucyl-V caused accumulation of N-acetylglucosamine-beta-1, 4-MurNAc-pentapeptide-pyrophosphoryl-undecaprenol (lipid II). These data show that CBP-desleucyl-V inhibits peptidoglycan synthesis at the transglycosylation stage in the absence of binding to dipeptide.

Macrolide transport in Escherichia coli strains having normal and altered OmpC and/or OmpF porins.

[(14)C]Erythromycin and [(14)C]azithromycin uptake rates were studied in Escherichia coli strains containing normal OmpC and OmpF porins (strain MRC 106) and altered OmpC porins due to small insertions (strains RAM121 and OC1555) or deletions (strain RAM122) in the ompC alleles and altered OmpF porins due to small ompF deletions (strains OC1555 and PLB3255). Strains RAM121 and RAM122 also lacked OmpF porins in their outer membrane. The porin mutants demonstrated a 2- to 1224-fold increase in macrolide transport and a concurrent 3- to 530-fold decrease in MIC when compared to the parent strain, MCR106. Both strains OC1555 and PLB3255 had enhanced permeability to 1-N-phenylnaphthylamine indicating increased permeability of the outer membrane to hydrophobic molecules. The macrolides, at 2 to 1000 times MIC, failed to displace the cationic probe polymyxin; therefore, drug entry by a self-promoted mechanism was not indicated. Since >95% of macrolide is protonated and thus hydrophilic (logP(i)=-0.89) at neutral pH, the bulk of drug entry may be via the porin channels.

Synthesis of hydrophobic N'-mono and N',N"-double alkylated eremomycins inhibiting the transglycosylation stage of bacterial cell wall biosynthesis.

A series of hydrophobic N'-mono and N',N"-double alkylated derivatives of the glycopeptide antibiotic eremomycin were synthesized by reductive alkylation after preliminary protection of the N-terminal amino group of the peptide backbone. The investigation of the antibacterial activity in vitro showed that N'-C10H21- and N'-p-(p-chlorophenyl)benzyl derivatives of eremomycin are the most active against vancomycin-resistant enterococci among the compounds obtained though they are less effective than the corresponding lipophilic derivatives of vancomycin. The introduction of two hydrophobic substituents led to a decrease in activity against both susceptible and resistant bacteria. The biochemical evaluation of the mode of action revealed that in addition to binding to D-Ala-D-Ala these compounds also have an alternative mechanism of action that does not require substrate binding.

Programs to facilitate tuberculosis drug discovery: the tuberculosis antimicrobial acquisition and coordinating facility.

There is a real need to discover new drugs that are active on drug-resistant tuberculosis (TB), and for drugs that will shorten the time of therapy. Large pharmaceutical companies have traditionally led the quest for discovering and developing new antiinfective agents but this is not the case when it comes to diseases like tuberculosis that primarily occur in resource restricted countries. Throughout the world many research groups are actively engaged in the scientific discovery of new TB drugs. Unfortunately, most research laboratories do not have the necessary safety facilities or resources for all facets of TB drug discovery. The Tuberculosis Antimicrobial Acquisition and Coordinating Facility (TAACF) was established in order to make comprehensive testing services available at no cost to research laboratories with an interest in discovering new TB drugs. The TAACF is a consortium of contracts managed and funded by the National Institute of Allergy and Infectious Diseases (National Institutes of Health, Bethesda, MD) as a resource to support preclinical drug discovery and development. The core of the TAACF is the Southern Research Institute, Birmingham, AL, which supports compound acquisition, storage, medicinal chemistry, and high throughput assays. Other collaborating groups provide biological data on antimycobacterial activity and cytotoxicity, preliminary in vivo toxicity, oral bioavailability and efficacy in animal models, specialty testing (such as activity against non-replicating persistent bacteria), and assistance in technology transfer for developing comprehensive promotional packages and facilitating partnerships with pharmaceutical companies for drug development. The TAACF program and recent progress that has been publicly disclosed by suppliers is reviewed. There are many aspects promising of the program that will not be discussed due to confidentially.

Bacillus subtilis spore coats: complexity and purification of a unique polypeptide component.

Extensively washed, dormant spores of Bacillus subtilis were disrupted with glass beads in buffer at pH 7 in the presence of protease inhibitors. Approximately 31% of the total spore protein was soluble, and another 14% was removed from the insoluble fraction by hydrolysis with lysozyme and washing with 1 M KCl and 0.1% sodium dodecyl sulfate. The residual spore integuments comprised 55% of the total spore proteins and consisted of coats and residual membrane components. Treatment of integuments with sodium dodecyl sulfate and reducing agents at pH 10 solubilized 40% of the total spore protein. Seven low-molecular-weight polypeptide components of this solubilized fraction comprised 27% of the total spore protein. They are not normal membrane components and reassociated to form fibrillar structures resembling spore coat fragments. The residual insoluble material (15% of the total spore protein) was rich in cysteine and was probably also derived from the spore coats. A solubilized coat polypeptide of molecular weight 12,200 has been purified in good yield (4 to 5% of the total spore protein). Five amino acids account for 92% of its total amino acid residues: glycine, 19%; tyrosine, 31%; proline, 23%; arginine, 13%; and phenylalanine, 6%.

Coat protein synthesis during sporulation of Bacillus subtilis: immunological detection of soluble precursors to the 12,200-dalton spore coat protein.

Antibody specific to the 12,200-dalton spore coat protein of Bacillus subtilis was used to detect the synthesis of cross-reacting material during sporulation. Cross-reacting protein was first detected by immunoprecipitation after 4 h of development and represented at least 1 to 2% of the total soluble protein synthesis at 5.5 h. A polypeptide of 21,000 daltons was detected in immunoprecipitates by gel electrophoresis. This polypeptide did not accumulate in sporulating cells and was rapidly turned over at the time of coat deposition. In contrast, a 32,000-dalton polypeptide reacted with antibody when unlabeled cell protein was denatured with sodium dodecyl sulfate, separated by gel electrophoresis, and transferred to nitrocellulose paper. This polypeptide was not detected during cell growth or the first 3.5 h of development but was found to accumulate in sporulating cells at 5.5 h. The lack of detection of this polypeptide by immunoprecipitation of undenatured protein indicates that the antigenic sites which cross-reacted with antibody to the 12,200-dalton protein sequence were not exposed unless the molecular conformation was altered. The 32,000-dalton protein may be a primary translation product which is proteolytically processed into mature spore coat protein via a 21,000-dalton intermediate.

Morphology and patterns of protein synthesis during sporulation of Bacillus subtilis Eryr spo(Ts) mutants.

Erythromycin-resistant (Eryr) mutants of Bacillus subtilis 168 fail to sporulate at high temperature (47 degrees C) but sporulate normally at 30 to 35 degrees C. They also fail to sporulate at any temperature in the presence of 2.5 micrograms of erythromycin per ml. Neither of these nonpermissive conditions appears to affect vegetative growth, and the periods of sensitivity to both conditions extend from 40 to 90% of the sporulation period. At 47 degrees C, net incorporation of methionine and phenylalanine in postexponential Eryr and 168 cells was similar, and fractionation of the labeled products by polyacrylamide gel electrophoresis gave patterns in which many of the bands produced by mutant and parental cells coincided. However, distinct differences were seen, and since no spore-specific morphogenesis occurred in the Eryr cells at 47 degrees C, a selective defect in spore gene expression was inferred. At 35 degrees C plus erythromycin, spore morphogenesis proceeded normally until forespores were produced and then ceased, coincident with a marked increase in sensitivity of total protein synthesis to erythromycin. The effects seem to be nonspecific, therefore, and may indicate a change in cell permeability or ribosomal sensitivity to erythromycin.

Molecular cloning of the structural gene coding for CTP:CMP-3-deoxy-manno-octulosonate cytidylyltransferase from Escherichia coli K-12.

The kdsB gene from Escherichia coli K-12, which encodes CTP:CMP-3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase), was cloned into pBR322 as an 8-kilobase PstI fragment. Selection of this cloned segment was facilitated by using Salmonella typhimurium SL5283, which is deficient in three restriction enzyme systems and thus allows efficient cloning of E. coli DNA in S. typhimurium. The temperature-sensitive kdsB gene from S. typhimurium HD2 was transduced into strain SL5283 after the insertion of transposon Tn10 near the kdsB allele. Tetracycline-sensitive variants of strain SL5283 were then derived and used to select clones of the E. coli K-12 gene, inserted into the PstI site of pBR322, by complementation of the temperature-sensitive lesion in kdsB. One plasmid, pRG-1, complemented the kdsB temperature-sensitive allele and had the following characteristics: (i) it coded for several polypeptides by coupled transcription-translation in vitro, including one polypeptide which comigrated with CMP-KDO synthetase during polyacrylamide gel electrophoresis in sodium dodecyl sulfate; (ii) it overproduced CMP-KDO synthetase activity 20- to 40-fold depending on strain and growth conditions; and (iii) it coded for activity of CMP-KDO synthetase which, when purified to homogeneity, had the same molecular weight and kinetic characteristics as CMP-KDO synthetase of chromosomal origin.

Isolation of Salmonella typhimurium strains that utilize exogenous 3-deoxy-D-manno-octulosonate for synthesis of lipopolysaccharide.

Spontaneous mutants of Salmonella typhimurium LT2 were selected for the ability to accumulate exogenous 3-deoxy-D-manno-octulosonate (KDO). Bacteria containing a gene (kdsA) which codes for a temperature-sensitive KDO-8-phosphate synthetase were plated at the restrictive temperature of 42 degrees C on medium containing 5 mM KDO. Since bacteria containing the kdsA lesion are unable to grow at 42 degrees C due to inhibition of lipopolysaccharide (LPS) synthesis and accumulation of lipid A precursor, this method allowed direct, positive selection of mutants capable of utilizing exogenous KDO for LPS synthesis. Spontaneous mutants, selected at a frequency of about 10(-6), required exogenous KDO for growth at 42 degrees C. The growth rate at 42 degrees C was nearly normal in the presence of 20 mM KDO and was directly proportional to KDO concentrations below 20 mM. Exogenous KDO also suppressed accumulation of lipid A precursor. The apparent Km for KDO accumulation was 23 mM, and the maximum rate of transport was calculated to be 505 pmol of KDO per min per 10(8) cells. Bacteria incorporated exogenous [3H]KDO exclusively into LPS, with less than 10% dilution in specific activity due to residual endogenous KDO synthesis. The mutation giving rise to the ability to accumulate exogenous KDO was extremely useful in the direct screening for new mutations in the kdsA gene after localized mutagenesis. Five mutations in kdsA were isolated, four of which were new alleles as determined by on fine-structure analysis. The ability to introduce labeled (3H, 13C, and 14C) KDO in vivo should simplify and extend the analysis of this critical metabolic pathway in gram-negative bacteria.

Role of an energy-dependent efflux pump in plasmid pNE24-mediated resistance to 14- and 15-membered macrolides in Staphylococcus epidermidis.

We have elucidated a new mechanism for bacterial resistance to the 14-membered macrolides oleandomycin and erythromycin and the 15-membered macrolide azithromycin. Plasmid pNE24, previously isolated from a clinical specimen of Staphylococcus epidermidis, was characterized as causing resistance to 14-membered but not 16-membered macrolides by a mechanism suggested to involve reduced antibiotic permeation of bacterial cells (B. C. Lampson, W. von David, and J. T. Parisi, Antimicrob. Agents Chemother. 30:653-658, 1986). Our recent investigations have demonstrated that S. epidermidis 958-2 containing plasmid pNE24 also contains an energy-dependent macrolide efflux pump which maintains intracellular antibiotic concentrations below those required for binding to ribosomes. Thus, when strain 958-2 was pretreated with the inhibitor carbonyl cyanide m-chlorophenylhydrazone (CCCP), macrolide accumulated at the same rate and to the same extent as in CCCP-treated or untreated control cells lacking plasmid pNE24 (strain 958-1). In contrast, macrolide did not accumulate in energy-competent strain 958-2 but did accumulate to levels equal to those of ribosomes immediately following CCCP addition. Furthermore, intracellular macrolide was excreted and bacteria resumed growth when CCCP but not macrolide was removed from the growth medium. As expected, the 16-membered macrolide niddamycin accumulated to the same level in energy-competent strains 958-1 and 958-2 at the same rapid rate. Macrolide incubated with lysates prepared from both strains or recovered from cells of strain 958-2 was unmodified and bound to ribosomes from strains 958-1 and 958-2 with identical affinities and kinetics, thus precluding a role for ribosome or drug alteration in the resistance mechanism. We conclude that the presence of plasmid pNE24 results in specific energy-dependent efflux of 14- and 15-membered macrolides.

Mechanism of O-antigen distribution in lipopolysaccharide.

O-antigen units are nonuniformly distributed among lipid A-core molecules in lipopolysaccharide (LPS) from gram-negative bacteria, as revealed by polyacrylamide gel electrophoresis in sodium dodecyl sulfate; the actual distribution patterns are complex, multimodal, and strain specific. Although the basic biochemical steps involved in synthesis and polymerization of O-antigen monomers and their subsequent attachment to lipid A-core are known, the mechanism by which specific multimodal distribution patterns are attained in mature LPS has not been previously considered theoretically or experimentally. We have developed probability equations which completely describe O-antigen distribution among lipid A-core molecules in terms of the probability of finding a nascent polymer (O antigen linked to carrier lipid) of length k (Tk) and the probability that a nascent polymer of length k will be extended to k + 1 by polymerase (pk) or transferred to lipid A-core by ligase (qk). These equations were used to show that multimodal distribution patterns in mature LPS cannot be produced if all pk are equal to p and all qk are equal to q, conditions which indicate a lack of selectivity of polymerase and ligase, respectively, for nascent O-antigen chain lengths. A completely stochastic model (pk = p, qk = q) of O-antigen polymerization and transfer to lipid A-core was also inconsistent with observed effects of mutations which resulted in partial inhibition of O-antigen monomer synthesis, lipid A-core synthesis, or ligase activity. The simplest explanation compatible with experimental observations is that polymerase or ligase, or perhaps both, have specificity for certain O-antigen chain lengths during biosynthesis of LPS. Our mathematical model indicates selectively probably was associated with the polymerase reaction. Although one may argue for a multimodal distribution pattern based on a kinetic mechanism i.e., varying reaction parameters in space or in time during cell growth, such a model requires complex sensory and regulatory mechanisms to explain the mutant data and mechanisms for sequestering specific components of LPS biosynthesis to explain the distribution pattern in normal cells. We favor the simple alternative of enzyme specificity and present generalized equations which should be useful in analysis of other analogous biochemical systems.

Complement attack of altered outer membrane areas synthesized after inhibition of the 3-deoxy-D-manno-octulosonate pathway leads to cell death.

Salmonella typhimurium containing specific genes coding for either temperature-sensitive (TS) 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate synthetase or TS cytidine monophosphate-KDO synthetase grow normally when incubated at 30 degrees C and are resistant to C-mediated killing. However, bacteria become avirulent and sensitive to C-mediated killing upon thermal inhibition of TS KDO-8-phosphate synthetase (incubation at 38 degrees C) or TS cytidine monophosphate-KDO synthetase (incubation at 42 degrees C). Such thermal inhibition concurrently causes synthesis of an altered outer membrane which we now show is the site that renders cells susceptible to C-mediated killing. After incubation of cells in serum, the altered outer membrane area contains C9 in a trypsin-resistant state and membrane attack complex (MAC) lesions observable by electron microscopy. Trypsin-resistant C9 and MAC lesions were also observed in the inner membrane fraction from such serum-treated cells. In contrast, little C9 and few MAC lesions were associated with unaltered outer membrane areas present on these same serum treated cells. Control cells, grown at 30 degrees C and treated with serum (1) bound one-fifth as much C9 as was bound to cells incubated at 42 degrees C, (2) contained only a rare MAC lesion in the outer membrane, and (3) no observable MAC lesions in the inner membrane. We conclude that the altered outer membrane area is the site that renders cells susceptible to insertion of the MAC into both the outer and inner membrane resulting in cell death.

Erythromycin and azithromycin transport into Haemophilus influenzae ATCC 19418 under conditions of depressed proton motive force (delta mu H).

The effect of collapsing the electrochemical proton gradient (delta mu H) on [3H]erythromycin and [14C]azithromycin transport in Haemophilus influenzae ATCC 19418 was studied. The proton gradient and membrane potential were determined from the distribution of [2-14C]dimethadione and rubidium-86, respectively. delta mu H was reduced from 124 to 3 mV in EDTA-valinomycin-treated cells at 22 degrees C with 150 mM KCl and 0.1 mM carbonyl cyanide m-chlorophenylhydrazone. During the collapse of delta mu H, macrolide uptake increased. Erythromycin efflux studies strongly suggested that this increase was not due to an energy-dependent efflux pump but was likely due to increased outer membrane permeability. These data indicated that macrolide entry was not a delta mu H-driven active transport process but rather a passive diffusion process.