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Penicillin-binding protein 2a (PBP2a) of Staphylococcus aureus is refractory to inhibition by available beta-lactam antibiotics, resulting in resistance to these antibiotics. The strains of S. aureus that have acquired the mecA gene for PBP2a are designated as methicillin-resistant S. aureus (MRSA). The mecA gene was cloned and expressed in Escherichia coli, and PBP2a was purified to homogeneity. The kinetic parameters for interactions of several beta-lactam antibiotics (penicillins, cephalosporins, and a carbapenem) and PBP2a were evaluated. The enzyme manifests resistance to covalent modification by beta-lactam antibiotics at the active site serine residue in two ways. First, the microscopic rate constant for acylation (k2) is attenuated by 3 to 4 orders of magnitude over the corresponding determinations for penicillin-sensitive penicillin-binding proteins. Second, the enzyme shows elevated dissociation constants (Kd) for the non-covalent pre-acylation complexes with the antibiotics, the formation of which ultimately would lead to enzyme acylation. The two factors working in concert effectively prevent enzyme acylation by the antibiotics in vivo, giving rise to drug resistance. Given the opportunity to form the acyl enzyme species in in vitro experiments, circular dichroism measurements revealed that the enzyme undergoes substantial conformational changes in the course of the process that would lead to enzyme acylation. The observed conformational changes are likely to be a hallmark for how this enzyme carries out its catalytic function in cross-linking the bacterial cell wall.

Beta-lactamases and penicillin-binding proteins are bacterial enzymes involved in antibiotic resistance to beta-lactam antibiotics and biosynthetic assembly of cell wall, respectively. Members of these large families of enzymes all experience acylation by their respective substrates at an active site serine as the first step in their catalytic activities. A Ser-X-X-Lys sequence motif is seen in all these proteins, and crystal structures demonstrate that the side-chain functions of the serine and lysine are in contact with one another. Three independent methods were used in this report to address the question of the protonation state of this important lysine (Lys-73) in the TEM-1 beta-lactamase from Escherichia coli. These techniques included perturbation of the pK(a) of Lys-73 by the study of the gamma-thialysine-73 variant and the attendant kinetic analyses, investigation of the protonation state by titration of specifically labeled proteins by nuclear magnetic resonance, and by computational treatment using the thermodynamic integration method. All three methods indicated that the pK(a) of Lys-73 of this enzyme is attenuated to 8.0-8.5. It is argued herein that the unique ground-state ion pair of Glu-166 and Lys-73 of class A beta-lactamases has actually raised the pK(a) of the active site lysine to 8.0-8.5 from that of the parental penicillin-binding protein. Whereas we cannot rule out that Glu-166 might activate the active site water, which in turn promotes Ser-70 for the acylation event, such as proposed earlier, we would like to propose as a plausible alternative for the acylation step the possibility that the ion pair would reconfigure to the protonated Glu-166 and unprotonated Lys-73. As such, unprotonated Lys-73 could promote serine for acylation, a process that should be shared among all active-site serine beta-lactamases and penicillin-binding proteins.

Production of low-affinity forms of penicillin-binding proteins (PBPs), although essential, is not sufficient to protect pneumococci against the inhibitory action of penicillin. Resistance also requires the newly identified protein MurM which, together with MurN, is involved with the synthesis of short peptide branches in the pneumococcal cell wall. Cells in which murM was inactivated produced cell walls without branches and also completely lost penicillin resistance. To understand these surprising observations a 3D-model of MurM was constructed, which helped to put into structural context several of the biochemical and genetic observations made about this protein.

Objective: To determine the prevalence of penicillin resistance and molecular characteristics of pneumococcal isolates at the University of Malaya Medical Center. Methods: From March 1999 to July 2000, 100 clinical isolates of Streptococcus pneumoniae were obtained from 93 patients of various ages and from various body sites. The minimum inhibitory concentrations (MICs) for penicillin and ceftriaxone were determined by E test, and results were interpreted according to guidelines recommended by the National Committee for Clinical Laboratory Standards (NCCLS). Fifty isolates were further serotyped, and analyzed by pulsed-field gel electrophoresis (PFGE) and polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP) of the penicillin-binding protein ( pbp ) 2b and 2x genes. Results: The majority of the isolates were from respiratory sites. Thirty-one isolates showed decreased susceptibility to penicillin (PRSP), and many of these also showed decreased susceptibility to ceftriaxone. Twelve serogroup/types (SGTs) were present, with 19F being the most common. PFGE analysis identified two dominant profiles, consisting mainly of PRSPs that had common serotypes (19F) and pbp gene patterns within their respective groups, although PCR-RFLP analysis showed different patterns of pbp genes among the PRSPs as compared to penicillin-susceptible strains, which had a uniform pattern. Conclusion: PRSPs were genetically related as shown by PFGE and serotype. The consistency of pbp gene patterns, observed among many of the PRSPs within their respective PFGE profiles, supported their relatedness as established by PFGE.

author, Penicillin binding protein (pbp) gene alterations of 328 clinical isolates of Streptococcus pneumoniae were examined for a correlation with their antibiotic-resistance. The frequency of penicillin G (PEN-G) resistance was determined to clarify susceptibility to several antibiotics, namely PEN-G, ampicillin, sulbactam/ampicillin, cefozopram, panipenem (PAPM), clarithromycin (CLR), azithromycin (AZM) and levofloxacin (LVX). Oligonucleotide primers for three pbp genes (pbp1a, pbp2x and pbp2b) were used to detect mutations in pbp. Of the strains, 25.9% were classified as Pen-G^s, 68.0% as Pen-G^ir and 6.1% as Pen-G^r. The polymerase chain reaction product for wild-type pbp1a was found in 185 isolates, that for wild-type pbp2x was found in 66 isolates and that for wild-type pbp2b was found in 213 isolates. None of these three genes was detectable in 100 isolates while all of them were detected in 64 isolates (1a^w/2x^w/2b^w). Of those 64 isolates with 1a^w/2x^w/2b^w, the minimum inhibitory concentration (MIC) of PEN-G was ≤0.06 mg/l for 54 isolates and 0.12 mg/l for 10 isolates. Of the 272 strains for which the MIC of PAPM was ≤0.03 mg/l, there were 85 Pen-G^s, 184 Pen-G^ir and three Pen-G^r isolates. Three strains for which the MIC of LVX was ≥4.0 mg/l included one Pen-G^s and two Pen-G^ir isolates. The MICs of CLR correlated significantly with those of AZM. The MIC of CLR was ≥1 mg/l for 216 isolates, and the MIC of AZM was ≥1 mg/l for 244 of them. These data suggested that PAPM may be effective against S. pneumoniae infection, although acquisition of resistance should be considered. LVX also seemed to be effective against S. pneumoniae.

The interaction of a moenomycin derivative with the enzyme penicillin binding protein 1b (PBP 1b) has been studied by means of STD NMR. The results obtained initiated the synthesis of a number of moenomycin derivatives modified in unit A including a moenomycin-ampicillin conjugate and determination of their antibiotic activities. A protocol is described that allows studying the interaction of moenomycin analogues with PBP 1b by fluorescence correlation spectroscopy.

Crystalline 1 (TAK-599) is a novel N-phosphono prodrug of anti-methicillin-resistant Staphylococcus aureus (MRSA) cephalosporin 2a (T-91825) that has high affinity for penicillin-binding protein (PBP) 2' (IC(50); 0.90 microg/mL) and shows potent in vitro anti-MRSA activity (MIC against MRSA N133; 1.56 microg/mL), comparable to that of vancomycin (1.56 microg/mL). Although 2a had insufficient water solubility (2.3 mg/mL) for parenteral administration, 1 showed excellent water solubility (>100 mg/mL, pH 7) as well as good chemical stability in the solid state and solution. In pharmacokinetic studies, when 1 was administered intravenously to rats and monkeys, it was rapidly converted into 2a in the blood. These results show that 1 (TAK-599) is a highly promising parenteral cephalosporin targeted for MRSA infection.

Staphylococci, a leading cause of infections worldwide, have devised two mechanisms for resistance to beta-lactam antibiotics. One is production of beta-lactamases, hydrolytic resistance enzymes, and the other is the expression of penicillin-binding protein 2a (PBP 2a), which is not susceptible to inhibition by beta-lactam antibiotics. The beta-lactam sensor-transducer (BlaR), an integral membrane protein, binds beta-lactam antibiotics on the cell surface and transduces the information to the cytoplasm, where gene expression is derepressed for both beta-lactamase and penicillin-binding protein 2a. The gene for the sensor domain of the sensor-transducer protein (BlaR(S)) of Staphylococcus aureus was cloned, and the protein was purified to homogeneity. It is shown that beta-lactam antibiotics covalently modify the BlaR(S) protein. The protein was shown to contain the unusual carboxylated lysine that activates the active site serine residue for acylation by the beta-lactam antibiotics. The details of the kinetics of interactions of the BlaR(S) protein with a series of beta-lactam antibiotics were investigated. The protein undergoes acylation by beta-lactam antibiotics with microscopic rate constants (k(2)) of 1-26 s(-1), yet the deacylation process was essentially irreversible within one cell cycle. The protein undergoes a significant conformational change on binding with beta-lactam antibiotics, a process that commences at the preacylation complex and reaches its full effect after protein acylation has been accomplished. These conformational changes are likely to be central to the signal transduction events when the organism is exposed to the beta-lactam antibiotic.

The chemical diversity of peptide and protein libraries generated from biological display systems is typically confined to the 20 naturally occurring amino acids. Here, we have developed a general strategy to introduce non-natural side chains into mRNA-display libraries via specific chemical derivatization. We constructed a mRNA-display library containing 3 × 1012 different peptides bearing a pendant penicillin moiety in a fixed position. In vitro selection using this hybrid peptide-drug library resulted in novel inhibitors of the Staphylococcus aureus penicillin binding protein 2a (PBP2a). This strategy resulted in a penicillin-peptide conjugate that has at least 100-fold higher activity than the parent penicillin itself. Our approach provides a convenient way to enhance the efficacy of known drugs and facilitates the discovery of powerful new hybrid ligands with functionalities beyond those provided by the 20 naturally occurring residues.

To clarify the state of methicillin-resistant coagulase-negative staphylococci (MRCNS) contamination in the hospital environment, we compared MRCNS isolated from the fingers of 40 nursing students who had not yet experienced clinical practice and 40 who had just completed clinical practice in the hospital. Fourteen MRCNS strains were detected in 13 students (32.5%) after clinical practice; Staphylococcus epidermidis in 9 students, Staphylococcus haemolyticus in 3, and Staphylococcus saprophyticus in 2. Drug sensitivity tests were performed, and the minimum inhibitory concentration (MIC) of penicillin-G (PCG) was more than 2 microg/ml in all strains, and that of ampicillin (ABPC) was more than 16 microg/ml in many strains. Only a few strains showed high MIC values for the other drugs tested. However, some Staphylococcus haemolyticus strains showed high MIC values for cefazolin (CEZ), arbekacin (ABK), gentamicin (GM), ofloxacin (OFLX), or imipenem (IPM). In all strains, the mecA gene was detected by polymerase chain reaction (PCR), and penicillin binding protein 2' (PBP2') was detected by the latex agglutination method. Methicillin-resistant Staphylococcus epidermidis (MRSE) isolated from the fingers of nursing students was compared with that isolated from blood culture specimens by arbitrarily primed (AP)-PCR analysis. The patterns obtained were different, a finding which excluded the presence of cross-infection. The present results show that basic preventive measures for cross-infection should be considered in the future, using such genetic analysis methods, so that MRCNS may not cause hospital infection.

The aim of this study was to compare the expression of oxacillin resistance in methicillin-resistant Staphylococcus aureus (MRSA) on Paper Disc Method agar supplemented with 5% defibrinated blood (PDM blood agar) and Mueller-Hinton agar supplemented with 2% NaCl (MH NaCl agar) using different susceptibility tests. Fifty mecA-containing isolates of S. aureus, exhibiting 46 different pulsed-field gel electrophoresis patterns, were comparatively tested using the E test, the single disk diffusion test, and the multipoint inoculation technique, under various culture conditions. The E test incubated at 35 degrees C for 24 h (breakpoint of resistanceor = 2.0 mg/L) detected 94% of the isolates on MH NaCl agar, compared with 28% for PDM blood agar (P0.05). The disk diffusion test (breakpoint10 mm in diameter) under these incubation conditions detected resistance in 100% of the isolates on MH NaCl agar and in 80% of the isolates on PDM blood agar (P0.05). The multipoint technique (breakpointor = 1 mg/L), applied at 35 degrees C for 24 h, detected 100% on MH NaCl agar and 46% on PDM blood agar (P0.05). Irrespective of the method of susceptibility testing evaluated, MH NaCl agar was superior to PDM blood agar for the detection of oxacillin resistance in mecA-containing S. aureus.

Brucella spp. L-forms have been proposed to be stationary phase organisms in the evolution of new variants and enduring entities in the host in complicated cases of brucellosis and during latent brucellosis. In vitro formation of Brucella L-forms has been achieved by treating the cells with sub-lethal doses of penicillin. Interestingly, Brucella spp. have classified during the evolution into two groups, penicillin susceptible or penicillin resistant, yet both types grow on 20 microg/ml of methicillin. Strains proven susceptible to penicillin grew in the presence of methicillin as L-forms as demonstrated by light and electron microscopy. In addition, the B. melitensis vaccine strain Rev.1, a penicillin susceptible organism, responded to sheep serum by development of L-form-like structures unlike wild type, strain 16M. The two strains grew normally in sheep macrophages. We propose, for the first time, a model that associates Brucella pathogenicity with the structure and activity of two of their penicillin binding proteins (PBPs). According to the model, PBP1 has evolved as the major cell wall synthesizing enzyme of the genus, capable of responding to host serum growth factor(s) necessary for Brucella survival in the host. This property is associated with high avidity to beta-lactam antibiotics. PBP2 complements the activity of PBP1. New beta-lactam antibiotics and improved vaccines might be developed based on this property.

Penicillin-binding proteins (PBPs), the target enzymes of β-lactam antibiotics such as penicillins and cephalosporins, catalyze the final peptidoglycan cross-linking step of bacterial cell-wall biosynthesis. β-Lactams inhibit this reaction because they mimic the d -alanyl- d -alanine peptide precursors of cell-wall structure. Prior crystallographic studies have described the site of β-lactam binding and inhibition, but they have failed to show the binding of d -Ala- d -Ala substrates. We present here the first high-resolution crystallographic structures of a PBP, d -Ala- d -Ala-peptidase of Streptomyces sp. strain R61, non-covalently complexed with a highly specific fragment (glycyl- l -α-amino-e-pimelyl- d -Ala- d -Ala) of the cell-wall precursor in both enzyme–substrate and enzyme–product forms. The 1.9 A resolution structure of the enzyme–substrate Henri–Michaelis complex was achieved by using inactivated enzyme, which was formed by cross-linking two catalytically important residues Tyr159 and Lys65. The second structure at 1.25 A resolution of the uncross-linked, active form of the dd -peptidase shows the non-covalent binding of the two products of the carboxypeptidase reaction. The well-defined substrate-binding site in the two crystallographic structures shows a subsite that is complementary to a portion of the natural cell-wall substrate that varies among bacterial species. In addition, the structures show the displacement of 11 water molecules from the active site, the location of residues responsible for substrate binding, and clearly demonstrate the necessity of Lys65 and or Tyr159 for the acylation step with the donor peptide. Comparison of the complexed structures described here with the structures of other known PBPs suggests the design of species-targeted antibiotics as a counter-strategy towards β-lactamase-elicited bacterial resistance.

We isolated 55 coagulase-negative staphylococci (CoNS) over two separate 12-month periods (26 in 1993 and 29 in 1996) from the blood of neonates in a neonatal intensive case unit (NICU) in Melbourne, Australia and compared them by pulse-field gel electrophoresis profile (PFGE), random amplification of polymorphic DNA (RAPD) and antibiogram. The most common species were Staphylococcus epidermidis, S. haemolyticus and S. warneri. The majority of such isolates were resistant to penicillin and to either or both of methicillin and gentamicin. During 1993, there was an increase in the number of CoNS bloodstream infections compared with previous years. S. epidermidis was the most common isolate, with 88% assessed as clinically relevant. Using the three typing systems, we identified one likely epidemic clone of S. epidermidis, the isolates of which were resistant to penicillin, gentamicin and erythromycin and possessed the mecA gene. There was complete correlation between the detection of mecA and the phenotypic expression of resistance when zone diameters in the disc diffusion assay were interpreted according to the latest NCCLS guidelines (1999). Profiles of the remaining 1993 isolates were generally heterogeneous, suggesting independent acquisition with some evidence of cross-infection. The predominant bloodstream isolates in 1996 were heterogeneous multi-resistant strains of S. epidermidis, S. haemolyticus and S. warneri, about half of which were assessed as clinically relevant. These data support the view that CoNS are significant nosocomial pathogens in NICU and that resistant clones may be transmitted between babies. Molecular epidemiological tools are helpful for understanding transmission patterns and sources of infection, and are useful for measuring outcomes of intervention strategies implemented to reduce nosocomial CoNS sepsis. PFGE was found to be more discriminatory than RAPD, but the latter provides results in a more timely manner.

Summary Background A new type of meticillin-resistant Staphylococcus aureus (MRSA), designated community-acquired MRSA, is becoming increasingly noticeable in the community, some strains of which cause fatal infections in otherwise healthy individuals. By contrast with hospital-acquired MRSA, community-acquired MRSA is more susceptible to non β-lactam antibiotics. We investigated the high virulence potential of certain strains of this bacterium. Methods We ascertained the whole genome sequence of MW2, a strain of community-acquired MRSA, by shotgun cloning and sequencing. MW2 caused fatal septicaemia and septic arthritis in a 16-month-old girl in North Dakota, USA, in 1998. The genome of this strain was compared with those of hospital-acquired MRSA strains, including N315 and Mu50. Findings Meticillin resistance gene ( mecA ) in MW2 was carried by a novel allelic form (type IVa) of staphylococcal cassette chromosome mec (SCC mec ), by contrast with type II in N315 and Mu50. Type IVa SCC mec did not carry any of the multiple antibiotic resistance genes reported in type II SCC mec . By contrast, 19 additional virulence genes were recorded in the MW2 genome. All but two of these virulence genes were noted in four of the seven genomic islands of MW2. Interpretation MW2 carried a range of virulence and resistance genes that was distinct from those displayed on the chromosomes of extant S aureus strains. Most genes were carried by specific allelic forms of genomic islands in the MW2 chromosome. The combination of allelic forms of genomic islands is the genetic basis that determines the pathogenicity of medically important phenotypes of S aureus , including those of community-acquired MRSA strains.

Oxacillin resistance was examined in 258 coagulase-negative staphylococci from Greek hospitals. mecA DNA was detected in 168 isolates, which were also resistant to oxacillin by agar dilution and disk diffusion, according to the current NCCLS breakpoints. Both methods exhibited a relatively low specificity misclassifying 21 and 19 of the 90 mecA-negative isolates respectively as oxacillin resistant. In contrast, an anti-PBP 2a latex agglutination test, applied after induction by oxacillin, correctly classified 163 mecA-positive (sensitivity 97%) and 88 mecA-negative isolates (specificity 97.7%).

One hundred and ninety-three isolates of coagulase-negative staphylococci (CoNS) were tested against oxacillin by agar dilution, disk diffusion, and Vitek (GPS-105 card), and the presence of the mecA gene determined by multiplex PCR. The results obtained by all testing methods were in agreement for 190 isolates. Two mecA -negative isolates ( S. lugdunensis and S. haemolyticus ) had MICs of ≤0.25 μg/ml by agar dilution and Vitek but were resistant by disk diffusion. One mecA -positive isolate was resistant by Vitek and disk diffusion but had an agar dilution MIC of ≤0.25 μg/ml. For the species of CoNS tested, oxacillin susceptibility results obtained with the Vitek GPS-105 card and disk diffusion correlated well with results obtained by National Committee for Clinical Laboratory Standards agar dilution and with the presence of the mecA gene.

A benzyl alcohol-guanidine hydrochloride extraction method was used to remove sodium polyanetholesulfonate present in BacT/Alert blood culture bottles. Multiplex PCR using touchdown annealing was used to detect the mecA, nuc, and 16S rRNA genes in bottles growing staphylococci. This direct PCR assay demonstrated excellent sensitivity, specificity and improved accuracy compared to routine phenotypic methods for determination of methicillin resistance in coagulase negative staphylococci (CoNS). However, with this PCR assay, bottles that contained both methicillin-resistant CoNS and methicillin-susceptible Staphylococcus aureus would be misidentified as containing methicillin-resistant S. aureus.

Significant advances have been made in recent years in our understanding of how methicillin resistance is acquired by Staphylococcus aureus . Integration of a staphylococcal cassette chromosome mec (SCC mec ) element into the chromosome converts drug-sensitive S . aureus into the notorious hospital pathogen methicilin-resistant S . aureus (MRSA), which is resistant to practically all β-lactam antibiotics. SCC mec is a novel class of mobile genetic element that is composed of the mec gene complex encoding methicillin resistance and the ccr gene complex that encodes recombinases responsible for its mobility. These elements also carry various resistance genes for non-β-lactam antibiotics. After acquiring an SCC mec element, MRSA undergoes several mutational events and evolves into the most difficult-to-treat pathogen in hospitals, against which all extant antibiotics including vancomycin are ineffective. Recent epidemiological data imply that MRSA has embarked on another evolutionary path as a community pathogen, as at least one novel SCC mec element seems to have been successful in converting S . aureus strains from the normal human flora into MRSA.

In Alzheimer's disease and spongiform encephalopathies proteins transform from their native states into fibrils. We find that several amyloid-forming proteins harbor an alpha-helix in a polypeptide segment that should form a beta-strand according to secondary structure predictions. In 1324 nonredundant protein structures, 37 beta-strands with > or =7 residues were predicted in segments where the experimentally determined structures show helices. These discordances include the prion protein (helix 2, positions 179-191), the Alzheimer amyloid beta-peptide (Abeta, positions 16-23), and lung surfactant protein C (SP-C, positions 12-27). In addition, human coagulation factor XIII (positions 258-266), triacylglycerol lipase from Candida antarctica (positions 256-266), and d-alanyl-d-alanine transpeptidase from Streptomyces R61 (positions 92-106) contain a discordant helix. These proteins have not been reported to form fibrils but in this study were found to form fibrils in buffered saline at pH 7.4. By replacing valines in the discordant helical part of SP-C with leucines, an alpha-helix is found experimentally and by secondary structure predictions. This analogue does not form fibrils under conditions where SP-C forms abundant fibrils. Likewise, when Abeta residues 14-23 are removed or changed to a nondiscordant sequence, fibrils are no longer formed. We propose that alpha-helix/beta-strand-discordant stretches are associated with amyloid fibril formation.

Penicillin-binding protein 5 (PBP 5) of Escherichia coli functions as a d-alanine carboxypeptidase, cleaving the C-terminal d-alanine residue from cell wall peptides. Like all PBPs, PBP 5 forms a covalent acyl-enzyme complex with beta-lactam antibiotics; however, PBP 5 is distinguished by its high rate of deacylation of the acyl-enzyme complex (t(12) approximately 9 min). A Gly-105 --Asp mutation in PBP 5 markedly impairs this beta-lactamase activity (deacylation), with only minor effects on acylation, and promotes accumulation of a covalent complex with peptide substrates. To gain further insight into the catalytic mechanism of PBP 5, we determined the three-dimensional structure of the G105D mutant form of soluble PBP 5 (termed sPBP 5') at 2.3 A resolution. The structure is composed of two domains, a penicillin binding domain with a striking similarity to Class A beta-lactamases (TEM-1-like) and a domain of unknown function. In addition, the penicillin-binding domain contains an active site loop spatially equivalent to the Omega loop of beta-lactamases. In beta-lactamases, the Omega loop contains two amino acids involved in catalyzing deacylation. This similarity may explain the high beta-lactamase activity of wild-type PBP 5. Because of the low rate of deacylation of the G105D mutant, visualization of peptide substrates bound to the active site may be possible.

A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as "receptor-binding domains" (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59-80 % were detected as RBDs. A statistical analysis of amino acid frequencies was carried out in known interaction sites and in predicted RBDs. RBDs were predicted from the 80,000 sequences of the Swissprot database. In both cases, arginine is the most frequently occurring residue. The RBD procedure can also detect residues involved in specific interaction sites such as the DNA-binding (95 % detected) and Ca-binding domains (83 % detected). We report two recent analyses; from the prediction of RBDs in sequences to the experimental demonstration of the functional activities. The examples concern a retroviral Gag protein and a penicillin-binding protein. We support that this method is a quick way to predict protein interaction sites from sequences and is helpful for guiding experiments such as site-specific mutageneses, two-hybrid systems or the synthesis of inhibitors.

The prfA genes of Bacillus stearothermophilus and Bacillus subtilis are in an operon downstream of the ponA gene encoding penicillin-binding protein 1 (PBP1), a major enzyme involved in peptidoglycan synthesis. The specific function of the 23- to 24-kDa PrfA protein is unknown but this protein plays some role in nucleoid segregation and the functions of PrfA and PBP1 are interrelated. We overexpressed B. stearothermophilus and B. subtilis PrfA in Escherichia coli and purified the proteins to homogeneity by cation exchange and gel filtration chromatography. The protein is a monomer in solution, and circular dichroism spectroscopy revealed an abundance of β-sheet secondary structure. Crystals of B. stearothermophilus PrfA were also obtained and diffracted X-rays to 1.8 A resolution.

The peptidoglycan structure of in vitro selected ampicillin-resistant mutant Enterococcus faecium D344M512 and of the susceptible parental strain D344S was determined by reverse phase high performance liquid chromatography and mass spectrometry. The muropeptide monomers were almost identical in the two strains. The substantial majority (99.3%) of the oligomers from the susceptible strain D344S contained the usual d-alanyl --> d-asparaginyl (or d-aspartyl)-l-lysyl cross-link (d-Ala --> d-Asx-l-Lys) generated by beta-lactam-sensitive DD-transpeptidation. The remaining oligomers (0.7%) were produced by beta-lactam-insensitive LD-transpeptidation, because they contained l-Lys --> d-Asx-l-Lys cross-links. The muropeptide oligomers of the ampicillin-resistant mutant D344M512 contained only these l-Lys --> d-Asx-l-Lys cross-links indicating that resistance was due to the bypass of the beta-lactam-sensitive DD-transpeptidation reaction. The discovery of this novel resistance mechanism indicates that DD-transpeptidases cannot be considered anymore as the sole essential transpeptidase enzymes.

The Bacillus subtilis genome sequencing project [Kunst et al., Nature 390 (1997) 249-256] identified ywhE as a gene that potentially encodes a high-molecular-weight class A penicillin-binding protein. Analysis of the expression of a translational ywhE-lacZ fusion showed that ywhE expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor sigma(F), and to a lesser extent by sigma(G). Primer extension analysis identified two transcription start sites located 26 and 27 nucleotides upstream of the ywhE translational initiation codon. Sequences located in the -10 and -35 regions relative to the transcription start sites showed good homology to the consensus sequences for promoter elements of sigma(F)-dependent genes. An insertional mutation in ywhE had no significant effect on growth, morphology, and sporulation, and ywhE spores had normal heat-resistance, cortex structure, and germination and outgrowth properties. However, overexpression of ywhE in Escherichia coli resulted in cell lysis.

A novel gene, drp35, of Staphylococcus aureus, which was inducible especially with cell wall-affecting antibiotics, has been cloned. Analysis of differential hybridization with mRNAs enhanced in the presence of beta-lactams resulted in two positive clones that harbored a new gene encoding a 35,845-Da protein (Drp35) and the penicillin-binding protein 2 (PBP2). Immunoblot analysis revealed that the Drp35 protein band was evidently enhanced after 30 min in the presence of beta-lactams. The Drp35 expression was also enhanced with not only beta-lactams, but also vancomycin, bacitracin, and fosfomycin. Homology search revealed that Drp35 was a new protein. Our results revealed that it was specific in S. aureus and respondent to these agents in both methicillin-resistant and -sensitive strains of S. aureus.

Penicillin-binding proteins (PBPs), targets of beta-lactam antibiotics, are membrane-bound enzymes essential for the biosynthesis of the bacterial cell wall. PBPs possess transpeptidase and transglycosylase activities responsible for the final steps of the bacterial cell wall cross-linking and polymerization, respectively. To facilitate our structural studies of PBPs, we constructed a 5'-truncated version (lacking bp from 1 to 231 encoding the N-terminal part of the protein including the transmembrane domain) of the pbp2a gene of Streptococcus pneumoniae and expressed the truncated gene product as a GST fusion protein in Escherichia coli. This GST fusion form of PBP2a, designated GST-PBP2a*, was expressed almost exclusively as inclusion bodies. Using a combination of high- and low-speed centrifugation, large amounts of purified inclusion bodies were obtained. These purified inclusion bodies were refolded into a soluble and enzymatically active enzyme using a single-step refolding method consisting of solubilization of the inclusion bodies with urea and direct dialysis of the solubilized preparations. Using these purification and refolding methods, approximately 37 mg of soluble GST-PBP2a* protein was obtained from 1 liter of culture. The identity of this refolded PBP2a* protein was confirmed by N-terminal sequencing. The refolded PBP2a*, with or without the GST-tag, was found to bind to BOCILLIN FL, a beta-lactam, and to hydrolyze S2d, an analog of the bacterial cell wall stem peptides. The S2d hydrolysis activity of PBP2a* was inhibited by penicillin G. In conclusion, using this expression system, and the purification and refolding methods, large amounts of the soluble GST-PBP2a* protein were obtained and shown to be enzymatically active.

Both vancomycin- and teicoplanin-resistant laboratory mutants of Staphylococcus aureus produce peptidoglycans of altered composition in which the proportion of highly cross-linked muropeptide species is drastically reduced with a parallel increase in the representation of muropeptide monomers and dimers (Sieradzki, K., and Tomasz, A. (1997) J. Bacteriol. 179, 2557-2566; and Sieradzki, K. , and Tomasz, A. (1998) Microb. Drug Resist. 4, 159-168). We now report that the distorted peptidoglycan composition is related to defects in penicillin-binding protein 4 (PBP4); no PBP4 was detectable by the fluorographic assay in membrane preparations from the mutants, and comparison of the sequence of pbp4 amplified from the mutants indicated disruption of the gene by two types of abnormalities, a 17-amino acid long duplication starting at position 305 of the pbp4 gene was detected in the vancomycin-resistant mutant, and a stop codon was found to be introduced into the pbp4 KTG motif at position 261 in the mutant selected for teicoplanin resistance. Additional common patterns of disturbances in the peptidoglycan metabolism of the mutants are indicated by the increased sensitivity of mutant cell walls to the M1 muramidase and decreased sensitivity to lysostaphin, which is a reversal of the susceptibility pattern of the parental cell walls. Furthermore, the results of high performance liquid chromatography analysis of lysostaphin digests of peptidoglycan suggest an increase in the average chain length of the glycan strands in the peptidoglycan of the glycopeptide-resistant mutants. The increased molar proportion of muropeptide monomers in the cell wall of the glycopeptide-resistant mutants should provide binding sites for the "capture" of vancomycin and teicoplanin molecules, which may be part of the mechanism of glycopeptide resistance in S. aureus.

A novel method has been developed for the detection of the mecA gene, that confers the principle mechanism of methicillin resistance in staphylococci. Cycling Probe Technology (CPT) is a rapid, simple, isothermal method for the detection of specific target sequences. CPT utilizes a unique chimeric DNA-RNA-DNA probe sequence that provides an RNase H sensitive scissile link when hybridized to a complementary target DNA sequence. In the presence of target DNA, the cycling reaction converts full-length chimeric probe into cleaved probe fragments, which accumulate and are quantified. A cycling probe designed for detection of a specific sequence within the mecA gene was used to develop a culture confirmation assay for methicillin resistant Staphylococcus aureus . The CPT assay was used to screen 238 S. aureus isolates and the results were in complete agreement with detection of the mecA gene by polymerase chain reaction (PCR). Detection of mecA should be considered the gold standard for determining methicillin resistance in S. aureus . This study demonstrates the feasibility of using CPT to meet this need.

A Cycling Probe Technology (CPT) assay was developed for the detection of the mecA gene from methicillin resistant staphylococcal cultures. The assay is based on a colorimetric enzyme-immuno-assay (EIA) and uses a mecA probe (DNA-RNA-DNA) labeled with fluorescein at the 5'-terminus and biotin at the 3'-terminus. The reaction occurs at a constant temperature that allows the target DNA to anneal to the probe. RNase H cuts the RNA portion, allowing the cut fragments to dissociate from the target, making it available for further cycling. CPT-EIA uses streptavidin-coated microplate wells to capture uncut probe followed by detection with horseradish-peroxidase conjugated anti-fluorescein antibody. The assay was compared to PCR and shown to accurately detect the presence or absence of the mecA gene in 159 staphylococcal clinical isolates. The CPT-EIA assay takes two hours starting from cultured cells compared with the 24-48 h required for detection of methicillin resistance by conventional susceptibility tests.

To examine contamination of donor eye preservation media with methicillin-resistant Staphylococcus aureus (MRSA), we studied the media to detect specific genes for MRSA by use of the polymerase chain reaction (PCR) method. The materials were 36 samples of donor eye preservation media (EP-II) in which donor eyes had been stored for keratoplasty. Polymerase chain reaction procedures were carried out to simultaneously detect the spa gene, which codes protein A of S. aureus, and the mecA gene, which codes penicillin-binding protein-2' contributing resistance to methicillin. Along with PCR analyses, the preservation media was examined by conventional culture methods to determine bacteriologic contamination. The PCR analyses of the 36 samples revealed that both the spa and the mecA genes were positive in five samples, only the spa gene was positive in two, and only the mecA gene was positive in two. The conventional culture of the media showed positive for MRSA in 5 samples, methicillin-susceptible S. aureus (MSSA) in 2, methicillin-susceptible coagulase-negative staphylococci (MS-CNS) in 4, and methicillin-resistant coagulase-negative staphylococci (MR-CNS) in 2 of the 36 samples. The results of PCR coincided well with those of conventional bacteriologic culture. Polymerase chain reaction analysis for spa and mecA genes is useful in detecting contamination of donor eye preservation media by MRSA, MSSA, MR-CNS, or MS-CNS in a shorter time than by conventional culture.

A new series of 1β-methyl carbapenems, in which a disubstituted-aminothiocarbonylthio moiety was attached to the C-2 position of the carbapenem nucleus, were prepared and evaluated for anti-MRSA activity. These derivatives showed good in vitro antibacterial activity against high-level MRSA, and the finding of good affinity for PBP-2′ supported these results. Some of the compounds having favorable protein-binding affinity showed excellent in vivo anti-MRSA activity.

A series of cephalosporin derivatives with various bicyclic heterocycles at the C-3 position was synthesized and evaluated for antibacterial activity. Among them CP0467 (3a) showed excellent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) (MIC90 = 6.25 microg/mL), and extremely high affinity for the penicillin binding protein 2' of MRSA (I50 = 0.49 microg/mL). Furthermore, 3a showed a long-acting pharmacokinetic profile in mice (AUC(infinity) = 482.3 microg/h/mL and T(1/2) = 1.9 h).

The clinical introduction of antimicrobial agents led to dramatic improvements in our ability to successfully treat serious bacterial infections in patients. Previously fatal diseases, such as endocarditis and meningitis, became medically treatable in a significant number of cases. The discovery of antibiotics was also accompanied by the emergence of bacteria resistant to these compounds, either through the mutation of cellular genes (as seen with the emergence of resistance to rifampin) or through the acquisition of novel resistance determinants (such as the staphylococcal [3-1actamase gene or the enterocoCccal vancomycin resistance

Laboratory mutants of Staphylococcus aureus strain ATCC 8325 (27S) selected for increased minimal inhibitory concentration (MIC) values to methicillin and cefotaxime showed increased rates of cell wall turnover and detergent-induced autolysis in virtual parallel with the increasing MIC for the antibiotic. Also in parallel with the increasing MICs for the particular antibiotic used in the selection was the gradual accumulation of an unusual muropeptide in the peptidoglycan of the mutants, muropeptide 12, which is a minor component of the cell wall of the parental strain. Analysis of muropeptide 12, its peptide derivative, and its lysostaphin degradation products by high pressure liquid chromatography, Edman degradation, and mass spectrometry suggests that muropeptide 12 is a dimer in which the two monomeric components are interlinked by two pentaglycyl cross-bridges, thus generating a 14-member macrocyclic ring structure. This unusual cross-linked structure may be the product of the abnormal activity of penicillin-binding protein 2 which has grossly reduced antibiotic binding capacity in the mutant staphylococci.

The Escherichia coli low molecular mass penicillin-binding proteins (PBP4, PBP5 and PBP6) are a group of penicillin-sensitive enzymes involved in the final stages of cell wall assembly. It has been suggested that these proteins may interact with the periplasmic face of the inner membrane via C-terminal amphiphilic alpha-helices. Theoretical analysis has predicted that these C-terminal helical regions may be membrane interactive. We have tested this hypothesis by assaying PBP C-terminal homologues (P4, P5 and P6) for haemolytic activity. Our results show that the PBP5 and PBP6 C-terminal homologues readily lyse sheep erythrocytes in a pH-dependent manner with LD50's of 3.5 x 10(-6) M and 6.8 x 10(-7) M respectively at pH 7. These results appear to support the present model for the membrane anchoring of PBP5 and PBP6. The PBP4 C-terminal homologue shows no evidence of haemolytic activity which could imply a different means of membrane association for PBP4.

Nearly all clinical isolates of methicillin resistant Staphylococcus aureus (MRSA) produce beta-lactamase as well as an additional low-affinity penicillin-binding protein called PBP2a or PBP2', the main factor for mediating methicillin resistance. Polidocanol (PDO), a dodecyl polyethyleneoxide ether, resensitizes clinical isolates of MRSA to methicillin; in addition, their resistance to benzylpenicillin (BP) is reduced. The action of PDO is based on the inhibition of the induced syntheses of PBP2a and beta-lactamase. Induction in our study was performed with 2-(2'-carboxyphenyl)benzoyl-6-aminopenicillanic acid (CBAP). Inducible PBP2a production in MRSA strains is under the control of the same regulatory system which is responsible for the induction of beta-lactamase synthesis. BlaR1, a membrane-spanning protein with a penicillin sensor and a signal transducer domain represents the starting point of this induction cascade. Based on its amphiphilic properties, it is likely that the action of PDO is located in the bacterial membrane. Therefore we investigated the possibility that BlaR1 might be the main target for PDO action. We were able to detect the BlaR1 sensor domain in resistant staphylococcal cells even in the noninduced state by fluorography. In a competition assay, CBAP was bound specifically, with a high affinity to the penicillin sensor. Moreover, the binding of CBAP was very stable. As concerns PDO, no significant interaction with the penicillin binding site of BlaR1 was detectable. This is why the BlaR1 transducer domain is thought to be the actual target area of PDO. In this case, PDO would interfere with the transmission of the signal, generated by the receptor binding of CBAP, through the membrane via BlaR1 into the staphylococcal cell. This assumption could be confirmed by the analysis of the concentration-effect relationship, whereafter PDO does not work as a competitive, but as a noncompetitive antagonist of CBAP. Our results demonstrate that BlaR1 could be an attractive new target for the development of new drugs to overcome methicillin resistance.

Resistance to beta-lactam antibiotics in some naturally transformable bacterial pathogens has arisen by interspecies recombinational events that have generated hybrid penicillin-binding proteins with reduced affinity for the antibiotics. This type of resistance is of particular concern in pneumococci, in which it is increasing worldwide.

Methicillin-resistant staphylococci have an additional low-affinity penicillin-binding protein, PBP2a (PBP2'), encoded by the mecA gene. The typical heterogeneity seen in the expression of resistance to methicillin and in levels of resistance depends on the concerted action of chromosomally encoded genes, including fem and aux, that are also present in the genome of susceptible staphylococci.

The radically altered cell-wall chemistry in penicillin-resistant pneumococci and the stringent requirement for specific cell-wall precursors for expression of high-level resistance to methicillin in staphylococci may represent compensating mechanisms to balance molecular risks produced by the strategies for antibiotic resistance in these bacteria.

A series of derivatives of phenyl phenylacetylglycinates (aryl phenaceturates) with a carboxylate substituent meta to the oxygen of the phenoxide leaving group and a functionalized methylene group in the ortho- or para-position have been synthesized. These molecules possess a latent o- or p-quinone methide electrophile which could be unmasked during enzymic turnover and could react with an active site nucleophile. This chemistry does seem to occur in solution where a common hydrolysis product, independent of the benzylic leaving group, presumably o- or p-hydroxymethylphenol, was observed. These depsipeptides are substrates of class A and C β-lactamases, particularly of the latter, comparable with the parent m-carboxyphenyl phenaceturate. They also have modest inhibitory activity against these enzymes and against the serine DD-peptidase of Streptomyces R61. The inhibition of a class C β-lactamase was turnover dependent, as expected of mechanism-based inhibitor, but the small leaving group dependence of the inhibition suggested that the quinone methide, if it was in fact responsible for the inhibition, was generated in solution subsequent to release of the product phenol from the active site.

The Bacillus subtilis spoVD gene has been cloned and sequenced. It encodes a 71,262 Da protein with extensive sequence similarity to penicillin-binding proteins from various organisms. The context of this gene in the B. subtilis chromosome, immediately upstream of the mur operon, suggests that it is related to the pbpB gene of Escherichia coli , which is involved in the synthesis of septal peptidoglycan during cell division. Expression of spoVD in E. coli leads to the synthesis of a membrane-associated protein of the size expected for SpoVD, which can bind labelled penicillin. However, insertional disruption of the spoVD gene has no effect on vegetative growth or division: a second pbp -like gene immediately upstream of spoVD is probably the functional homologue of E. coli pbpB. spoVD seems instead to have a specialized role in the morphogenesis of the spore cortex, which is a modified form of peptidoglycan. spoVD transcription appears to occur from a promoter recognized by the σ E form of RNA polymerase. Analysis of the expression of a spoVD'-lacZ reporter gene supports this notion and indicates that a second level of negative regulation is dependent on the SpoIIID protein. SpoVD synthesis probably occurs only in the mother cell since both σ E and SpoIIID are thought to be specific to this cell type. Such localization of SpoVD synthesis was supported by the results of a genetic test showing that expression of spoVD only in the mother cell is sufficient for spore formation. The results support the proposition that spore cortex formation is determined primarily by the mother cell.

The bacterial D-alanine carboxypeptidases (CPases) remove C-terminal D-alanyl residues from sugar-peptide cell wall precursors. The CPases have many characteristics in common with the high-M(r) penicillin-binding proteins (PBPs) whose inhibition by beta-lactam antibiotics is lethal. The CPases are attractive as model PBPs, because of their relatively lower M(r) and higher activity in vitro. We have cloned and sequenced the Bacillus stearothermophilus gene (dacA) coding for a membrane-bound CPase. The nucleotide (nt) sequence of the gene is homologous to that of the Escherichia coli and Bacillus subtilis dacA loci, which also code for membrane-bound CPases. E. coli host cells lysed when expression of B. stearothermophilus dacA was induced. The same coding sequence was expressed in the methylotrophic yeast, Pichia pastoris, using the alcohol oxidase-1 (AOX1) promoter. Over 100 micrograms/ml of CPase was efficiently secreted into the medium after induction by methanol, without adversely affecting this host. The yeast product is indistinguishable from the native enzyme in structure and activity. The ability to secrete large amounts of heterologous protein and the lack of endogenous peptidoglycan metabolism makes P. pastoris an attractive candidate for the production of PBPs.

The effects of mecillinam, ampicillin and cephalexin on peptidoglycan synthesis in Salmonella typhimurium 2616 have been studied at equivalent concentrations or "isoactivities". Using antibiotics at isoactivities allows a direct comparison of the biochemical effects of different antibiotics. When mecillinam was added at different times during the division cycle at a concentration that produced 50% inhibition of peptidoglycan synthesis in an exponential culture over a short period of time, the inhibition of synthesis was greatest in the newborn cells and least in the dividing cells. Antibiotic competition experiments showed that mecillinam preferentially bound to penicillin-binding protein 2 in S. typhimurium 2616. High performance liquid chromatography analysis of the residual peptidoglycan synthesized in the presence of mecillinam showed an unexpected increase in pentapeptides and a significant increase in cross-linking. Other antibiotics added at equivalent activities did not show an increase in cross-linking.

Resistance to teicoplanin in clinical isolates of Staphylococcus aureus has increased in frequency. Detection is difficult due to heterogeneous phenotypes of these strains. Two mutations in pbp4 have recently been identified in glycopeptide resistant laboratory strains. We investigated to determine if these mutations could be used to screen clinical isolates for teicoplanin resistance. Of 41 clinical isolates screened, none contained the mutations in pbp4 indicating these mutations cannot be used as a molecular diagnostic tool for glycopeptide resistance.

A rapid method for screening the affinity of proteins to dye-modified resins is described. Performing the binding and elution of the protein extracts in a batch-wise manner and eluting the bound proteins with SDS-PAGE denaturation buffer speed up the screening process and allow the analysis of large collections of dyes. Penicillin-binding protein 4 of Escherichia coli was used as a model enzyme to determine the influences of pH, metal ions, and ionic strength (0 to 500 mM NaCl) on its binding behavior using a collection of 98 dye-affinity resins.

A region of the Staphylococcus aureus chromosome has been isolated that contains the gene encoding penicillin-binding protein 4 (PBP4), as well as abcA , a gene that encodes a protein with strong, sequence similarity to the ABC transporter family of proteins. A disruption in abcA by Campbell-type integration results in cells that display an increased resistance to methicillin and cefoxitin, two antibiotics known to interact with low-molecular-weight PBPs. Based on these observations, a potential regulatory link between these two genes is discussed.

The interaction of representative beta-lactam antibiotics with a bacterial enzyme target has been mapped in three dimensions using X-ray diffraction data to 2.25 A resolution. Examination of complexes of cephalosporin C, benzylmonobactam, and alpha-(2,3)-methylenepenicillin G with the D-alanyl-D-alanine transpeptidase-carboxypeptidase from Streptomyces R61 shows that the enzyme's reactive serine has acylated the beta-lactam ring of each inhibitor. The known half-lives of the three acyl complexes can be correlated with the distance of the drug's carboxylate (or sulfonate) group from complementary groups on the DD-peptidase.

Imipenem (N-formimidoyl thienamycin, MK0787), a new carbapenem was found to have the widest antimicrobial activity of currently available beta-lactam drugs. Enterobacteriaceae had minimal inhibitory concentrations of imipenem of 8.0 micrograms/ml or less for 99.8 percent of clinical isolates. Only rare strains of Enterobacter species and Proteus mirabilis have higher imipenem minimal inhibitory concentration results. Hemophilus and Neisseria species were inhibited, but minimal inhibitory concentrations of imipenem were higher than those reported for third-generation cephalosporins. Only Pseudomonas maltophilia and Pseudomonas cepacia strains were imipenem resistant (MIC50 greater than 32 micrograms/ml) among the commonly isolated non-enteric gram-negative bacilli. All anaerobes were found susceptible to imipenem with the exception of some strains of Clostridium difficile. Staphylococcus species and non-enterococcal streptococci were very susceptible to imipenem. Streptococcus faecalis had higher minimal inhibitory concentrations of imipenem (MIC90 3.1 micrograms/ml) and S. faecium strains were frankly resistant. Methicillin-resistant S. aureus isolates had a MIC90 of 27.2 micrograms imipenem/ml. Imipenem was generally bactericidal except for marked minimal inhibitory and minimal bactericidal concentration differences with enterococci, Listeria, methicillin-resistant staphylococci, and some P. aeruginosa strains. The minimal inhibitory and minimal bactericidal concentrations of imipenem were not significantly influenced by organism inoculum size, probably because of its beta-lactamase stability to nearly all commonly encountered bacterial enzymes. Imipenem was found to be an excellent inhibitor of beta-lactamases and a potent enzyme inducer. The induction characteristic seems responsible for the antagonistic interactions of imipenem with some enzyme-labile beta-lactams in combination. Imipenem had limited stability in some in vitro susceptibility test systems. The 10 micrograms disk test or dry-form broth micro-dilution systems were preferred, applying the interpretive criteria from the National Committee for Clinical Laboratory Standards (M2-A3). Imipenem-resistant strains were rarely found in clinical practice and bacteria resistant to newer beta-lactams and aminoglycosides were generally very susceptible to this new carbapenem.