The recent availability of bacterial genome sequence information permits the identification of conserved genes that are potential targets for novel antibiotic drug discovery. Using a coupled bioinformatic/experimental approach, a list of candidate conserved genes was generated using a Microbial Concordance bioinformatics tool followed by a targeted disruption campaign. Pneumococcal sequence data allowed for the design of precise PCR primers to clone the desired gene target fragments into the pEVP3 'suicide vector'. An insertion-duplication approach was employed that used the pEVP3 constructs and resulted in the introduction of a selectable chloramphenicol resistance marker into the chromosome. In the case of non-essential genes, cells can survive the disruption and form chloramphenicol-resistant colonies. A total of 347 candidate reading frames were subjected to disruption analysis, with 113 presumed to be essential due to lack of recovery of antibiotic-resistant colonies. In addition to essentiality determination, the same high-throughput methodology was used to overexpress gene products and to examine possible polarity effects for all essential genes.

DNA probes consisting of pUC19 containing cloned Staphylococcus aureus chromosomal fragments were constructed from two methicillin-resistant S. aureus strains with diferent DNA sequences 5' to mecA, the gene that mediates methicillin resistance. The probe from one strain, BMS1, contained a portion of the regulatory sequences (the terminal 641 bp of mecRI and all of mecI) associated with the induction and repression of mecA transcription (pGO195). The second probe, from strain COL (pGO198), contained DNA not found in strain BMS1. This DNA was within the sequences added at the site of a mecRI deletion. epidermidis and all 20 S. haemolyticus isolates had from 5 to more than 20 additional chromosomal bands that hybridized with pGO198; none of 21 S. aureus isolates had additional hybridizing bands. These data suggest that the additional DNA responsible for the mecRi deletion was part of a repetitive, and possibly mobile, element resident in coagulase-negative staphylococci but not in S. aureus. These data also support a hypothesis that the deletion event occurred in a coagulase-negative staphylococcus with subsequent acquisition of the interrupted sequences by S. aureus.

Paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome are diseases of excess activation of the alternative pathway of complement that are treated with eculizumab, a humanized monoclonal antibody against the terminal complement component C5. Eculizumab must be administered intravenously, and moreover some patients with paroxysmal nocturnal hemoglobinuria on eculizumab have symptomatic extravascular hemolysis, indicating an unmet need for additional therapeutic approaches. We report the activity of two novel small-molecule inhibitors of the alternative pathway component Factor D using in vitro correlates of both paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome. Both compounds bind human Factor D with high affinity and effectively inhibit its proteolytic activity against purified Factor B in complex with C3b. When tested using the traditional Ham test with cells from paroxysmal nocturnal hemoglobinuria patients, the Factor D inhibitors significantly reduced complement-mediated hemolysis at concentrations as low as 0.01 μM. Additionally the compound ACH-4471 significantly decreased C3 fragment deposition on paroxysmal nocturnal hemoglobinuria erythrocytes, indicating a reduced potential relative to eculizumab for extravascular hemolysis. Using the recently described modified Ham test with serum from patients with atypical hemolytic uremic syndrome, the compounds reduced the alternative pathway-mediated killing of PIGA-null reagent cells, thus establishing their potential utility for this disease of alternative pathway of complement dysregulation and validating the modified Ham test as a system for pre-clinical drug development for atypical hemolytic uremic syndrome. Finally, ACH-4471 blocked alternative pathway activity when administered orally to cynomolgus monkeys. In conclusion, the small-molecule Factor D inhibitors show potential as oral therapeutics for human diseases driven by the alternative pathway of complement, including paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome.

The gene required for methicillin resistance in staphylococci, mecA, encodes the low-affinity penicillinbinding protein 2a (PBP2a). Transcriptional regulation of mecA is accomplished in some isolates by mecR1 and mecI, cotranscribed chromosomal genes that encode a putative signal transducer and a transcriptional repressor, respectively. Two Staphylococcus aureus strains that have identical mecR1-mecI nucleotide sequences, BMS1 and N315P, both exhibit low-level, heterotypic expression of methicillin resistance and contain no ␤-lactamase coregulatory sequences. mecR1-mecI was amplified from BMS1 by PCR and was shown to be functional on a high-copy-number plasmid when introduced into an S. aureus strain with a deleted mecR1-mecI locus. Cloned mecR1-mecI repressed phenotypic expression of methicillin resistance, mecA transcription and PBP2a production and mediated PBP2a induction in response to certain ␤-lactam antibiotics. However, mecR1-mecI had different regulatory activities in its native chromosomal location in N315P compared with those in BMS1. Uninduced mecA transcription was markedly repressed in N315P, and mecI inactivation increased mecA transcription and PBP2a production 5-and 40-fold, respectively. Furthermore, the N315P phenotype changed from low-level, heterotypic resistance with intact mecI to high-level, homotypic resistance in strains with disrupted mecI. In contrast, uninduced BMS1 produced abundant mecA transcript and PBP2a, while the disruption of mecI had no effect on phenotype and little effect on mecA transcription or PBP2a production. Thus, mecI-mediated repression of mecA appears to be dysfunctional in BMS1 because of the presence or absence of additional regulatory cofactors. Furthermore, heterotypic resistance expression in this strain is independent of mecA transcriptional regulation.Methicillin resistance, which encompasses resistance to all beta-lactam compounds, is a common phenotype among multiresistant, nosocomial staphylococci. Methicillin-resistant isolates are not effectively treated by most antibacterial agents and are a major challenge for chemotherapy. A low-affinity penicillin-binding protein (PBP), PBP2a, encoded by the chromosomally located gene mecA, mediates methicillin resistance among both Staphylococcus aureus and coagulase-negative staphylococci (13,30,44). PBP2a is expressed in addition to the normal complement of resident PBPs and remains the sole unsaturated PBP in the presence of beta-lactam antibiotics, alone capable of maintaining cell wall integrity. The mecA gene and Ն30 kb of flanking DNA are unique to methicillin resistant staphylococci; there are no allelic equivalents in methicillinsusceptible strains (2,8,23).Two methicillin resistance phenotypes are discernible by efficiency of plating (EOP) studies: homotypic and heterotypic (6,15,32). Homotypic (homogeneous) strains uniformly express high-level resistance, whereas heterotypic (heterogeneous) organisms exhibit a strain-unique variation in resistance expression. In heterotypic isolates, highly resistant s...

We describe the biological evaluation of isothiazoloquinolones (ITQs) having structural modifications at the 6-, 7-, and 8-positions. Addition of a methoxy substituent to C-8 effected an increase in antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and a decrease in cytotoxic activity against Hep2 cells. Removal of fluorine from C-6 or replacement of the C-8 carbon with a nitrogen compromised anti-MRSA activity. When the groups attached at C-7 were compared, the anti-MRSA activity decreased in the order 6-isoquinolinyl > 4-pyridinyl > 5-dihydroisoindolyl > 6-tetrahydroisoquinolinyl. The compound with the most desirable in vitro biological profile was 9-cyclopropyl-6-fluoro-8-methoxy-7-(2-methylpyridin-4-yl)-9H-isothiazolo[5,4-b]quinoline-3,4-dione (7g). This ITQ demonstrated (i) strong in vitro anti-MRSA activity (MIC90 = 0.5 microg/mL), (ii) strong inhibitory activities against S. aureus DNA gyrase and topoisomerase IV, with weak activity against human topoisomerase II, (iii) weak cytotoxic activities against three cell lines, and (iv) efficacy in an in vivo murine thigh model of infection employing MRSA.

Two D-glutamic acid biosynthetic activities, glutamate racemase and D-amino acid transaminase, have been described previously for bacteria. To date, no bacterial species has been reported to possess both activities. Genetic complementation studies using Escherichia coli WM335, a D-glutamic acid auxotroph, and cloned chromosomal DNA fragments from Staphylococcus haemolyticus revealed two distinct DNA fragments containing open reading frames which, when present, allowed growth on medium without exogenous D-glutamic acid. Amino acid sequences of the two open reading frames derived from the DNA nucleotide sequences indicated extensive identity with the amino acid sequence of Pediococcus pentosaceous glutamate racemase in one case and with that of the D-amino acid transaminase of Bacillus spp. in the second case. Enzymatic assays of lysates of E. coli WM335 strains containing either the cloned staphylococcal racemase or transaminase verified the identities of these activities. Subsequent DNA hybridization experiments indicated that Staphylococcus aureus, in addition to S. haemolyticus, contained homologous chromosomal DNA for each of these genes. These data suggest that S. haemolyticus, and probably S. aureus, contains genes for two D-glutamic acid biosynthetic activities, a glutamate racemase (dga gene) and a D-amino acid transaminase (dat gene).Most bacteria contain the macromolecular polymer peptidoglycan, which provides tensile strength to the cell wall (13). Peptidoglycan consists of alternating units of N-acetylglucosamine and N-acetylmuramic acid. Alternating L-and Damino acids are added by a set of unique enzymes to UDP-Nacetylmuramic acid to form the final cytoplasmic precursor of peptidoglycan (2, 13). One of the key D-amino acids, D-glutamic acid, has been found in earlier studies to have two different routes of biosynthesis. In Bacillus spp., D-glutamic acid is formed from D-alanine and ␣-ketoglutarate by a D-amino acid transaminase (EC 2.6.1.21) (14,22,24,25), while Lactobacillus spp., Pediococcus spp., and Escherichia coli use racemases which convert L-glutamic acid to D-glutamic acid (E. coli Dga [Glr, MurI]; EC 5.1.1.3) (3-6, 8, 9, 16, 23, 28). Attempts to detect either of these activities biochemically in most other bacteria, including medically important pathogens, have been limited and in some cases unsuccessful (17).Only one D-glutamic acid auxotrophic strain, E. coli WM335, has been reported (12, 15). Attempts to grow WM335 in the absence of exogenous D-glutamic acid result in rapid cell lysis. Using this strain as a recipient to screen a random Staphylococcus haemolyticus library, we observed in the work reported here that S. haemolyticus contains two distinct genes that complement the D-glutamic acid requirement of E. coli WM335. These genes, designated dga and dat, encode glutamate racemase and D-amino acid transaminase enzyme activities, respectively, as determined from in vivo complementation of D-glutamic acid auxotrophy, similarities at the amino acid level to previously reported sequences...

Clusters of peptidoglycan biosynthesis and cell division genes (DCW genes) were identified and sequenced in two gram-positive cocci, Staphylococcus aureus and Enterococcus faecalis. The results indicated some similarities in organization compared with previously reported bacterial DCW gene clusters, including the presence of penicillin-binding proteins at the left ends and ftsA and ftsZ cell division genes at the right ends of the clusters. However, there were also some important differences, including the absence of several genes, the comparative sizes of the div1B and ftsQ genes, and a wide range of amino acid sequence similarities when the genes of the gram-positive cocci were translated and compared to bacterial homologs.Biosynthesis of peptidoglycan in bacteria is a complex process involving numerous enzymes, most of which have been shown to be essential in pathogenic bacteria (3, 16). These enzymes have been studied most extensively in Escherichia coli, and the genes which encode them have been cloned and the proteins have been characterized over the past several years (29,30). Many of these genes had been previously mapped in this organism due to the availability of temperature-sensitive lethal mutants. In E. coli, it was discovered that a number of these genes, including the one encoding penicillin-binding protein 3 (PBP3), were organized in a cluster located at 2 min on the chromosomal map (29,34). Also present in this cluster were other genes important in cell division, including ftsA and ftsZ (4,19,31). All of these genes were found to be tightly packed, with reading frames sometimes overlapping, all oriented in the same direction of transcription, and there has been speculation about possible regulation of cellular growth and division within this region. Peptidoglycan biosynthetic genes were not exclusively in this 2-min region, however, as other genes, such as murA (69.3 min; 2), murB (89.9 min; 23), and murI (dga; 89.8 min; 10, 12), were found elsewhere on the chromosome.A cluster similar to the 2-min region of E. coli was found in the gram-positive rod Bacillus subtilis (6,27). Interestingly, with a few exceptions (for example, sporulation-specific genes), the gene arrangement was quite similar to that seen in E. coli, including the tight arrangement of genes and a similar direction of transcription (7,20). However, missing from this region and located elsewhere on the chromosome were the murC, murF, and ddl genes found in the E. coli cluster. Recently, the genome sequence of another gram-negative rod, Haemophilus influenzae, was reported and the gene order in this region was found to be identical to that of E. coli (13). These findings suggest a possible evolutionary relationship for genes involved in peptidoglycan biosynthesis and cell division.The existence of similar gene clusters in gram-positive cocci has not been reported. This work describes clusters of peptidoglycan biosynthetic and cell division genes in Staphylococcus aureus and Enterococcus faecalis, and the results presented show both...

We have previously shown (G. L. Archer, D. M. Niemeyer, J. A. Thanassi, and M. J. Pucci, Antimicrob. Agents Chemother. 38:447-454, 1994) that some methicillin-resistant staphylococcal isolates contain a partial deletion of the genes (mecR1 and mecI) that regulate the transcription of the methicillin resistance structural gene (mecA). When a fragment of DNA inserted at the point of the mecR1 deletion was used as a probe, hybridization with multiple bands was detected for Staphylococcus haemolyticus genomic DNA. In the present study, DNA sequencing of four unique clones recovered from a lambda library of S. haemolyticus revealed identical 1,934-bp elements. Each element, designated IS1272, contained 16-bp terminal inverted repeats (sequence identity, 15 of 16 bp) and two open reading frames of 819 and 687 bp; there were no flanking target site duplications. Database searches yielded amino acid homology with proteins predicted to be encoded by open reading frames from a putative insertion sequence element from Enterococcus hirae. DNA probes from each end and the middle of IS1272 were hybridized with restriction endonuclease-digested genomic DNA from clinical S. haemolyticus, Staphylococcus epidermidis, and Staphylococcus aureus isolates. Each of the 20 or more copies of the element found in S. haemolyticus isolates was intact, and copies were found in most chromosomal SmaI fragments. S. aureus and S. epidermidis isolates contained mostly incomplete fragments of the element, and there were many more hybridizing fragments in methicillin-resistant than in methicillin-susceptible isolates. IS1272, which appears to be primarily resident in S. haemolyticus, has disseminated to multiple staphylococcal species and is prevalent in multiresistant isolates.