SummaryTo address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, Staphylococcus aureus, using a rapid shotgun antisense RNA method. Staphylococcus aureus chromosomal DNA fragments were cloned into a xylose-inducible expression plasmid and transformed into S. aureus. Homology comparisons between 658 S. aureus genes identified in this particular antisense screen and the Mycoplasma genitalium genome, which contains 517 genes in total, yielded 168 conserved genes, many of which appear to be essential in M. genitalium and other bacteria. Examples are presented in which expression of an antisense RNA specifically reduces its cognate mRNA. A cell-based, drug-screening assay is also described, wherein expression of an antisense RNA confers specific sensitivity to compounds targeting that gene product. This approach enables facile assay development for high throughput screening for any essential gene, independent of its biochemical function, thereby greatly facilitating the search for new antibiotics.
An Escherichia coli mutant was isolated and shown to be polymyxin B resistant. Mapping and sequence analysis revealed a missense mutation at codon 53 within the pmrA (basR) gene that results in a G-to-V substitution. Fusions of promoters from the pmrC, yibD, and pmrH genes with the lacZ reporter showed that they were constitutively expressed in pmrA53 cells. In pmrA ؉ strains, these promoters were induced by iron and zinc, while a ⌬pmrA mutation blocked induction. The PmrA regulon regulates genes whose products remodel the composition and charge of lipid A and hence the barrier properties of the outer membrane. Along these lines, the pmrA53 mutant was also found to be hypersensitive to the anionic bile detergent deoxycholic acid.The outer membrane of gram-negative bacteria functions as a barrier to exclude toxic chemicals, such as antibiotics, from entering and killing the cell (18). To meet different environmental challenges, bacteria can physiologically adapt or mutate to remodel the chemical composition of lipopolysaccharides (LPS) and hence the permeability properties of their outer membranes (6, 16). In Salmonella enterica, pmrA constitutive mutants become resistant to the cationic antibiotic polymyxin B with the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and, to a lesser extent, phosphoethanolamine (pEtN) moieties to lipid A (9, 25). The addition of L-Ara4N partly neutralizes the negative charges on lipid A, a component of LPS, and hence reduces the electrostatic interaction with polymyxin B. Similarly, the PmrAB two-component regulon can be induced in wild-type cells by iron, which in turn leads to lipid A modification and polymyxin resistance (28). PmrAB-dependent remodeling of LPS also confers resistance towards cationic peptides and metal ions (4, 16). In Pseudomonas aeruginosa, polymyxinresistant mutants can be cross resistant to aminoglycosides (12).Inside the human host, LPS (endotoxin) remodeling plays a key role in bacterial fitness and virulence. L-Ara4N LPS modification not only confers resistance to endogenous antibacterial cationic peptides but also helps bacteria evade the innate immune system by making LPS a poor Toll-like receptor 4 agonist (16). To date, Salmonella has been the primary model organism for understanding the role of LPS remodeling in pathogenesis and antibiotic resistance. Here we identify and characterize a pmrA constitutive mutant of Escherichia coli and show that the mutant confers hypersensitivity to the bile detergent deoxycholic acid.Strains. During the course of our studies with novel antibacterial agents, we isolated a spontaneous resistant mutant named DW137 (Table 1) (D. Wall and J. M. Froelich, unpublished data). This mutation was mapped by Hfr crosses (15) to ϳ93 min on the E. coli chromosome. Subsequent bacteriophage P1vir transductions with a set of known Tn10 insertions around 93 min mapped the mutation between zje-2241::Tn10 and cadB2231::Tn10 (15, 17). Because the mutation mapped near the pmrAB (basRS) locus, we tested and found the strain was resistan...
Aminoglycoside antibiotics target an internal RNA loop within the bacterial ribosomal decoding site. Here, we described the synthesis and SAR of novel 3,5-diamino-piperidine derivatives as aminoglycoside mimetics, and show they act as inhibitors of bacterial translation and growth. KeywordsAminoglycosides; Antibiotics; Translation inhibitors; 2-deoxy-streptamine; Ribosome; Decoding site; 3; 5-diamino-piperidine Bacterial resistance to antibiotics is on the rise and represents a global medical threat. In hospitals in the United States, approximately two million patients per year are infected. 1 The majority of these nosocomial pathogens are resistant to at least one antibiotic and result in about 90,000 deaths per year; a number that has increased 7-fold over the last decade. The recent and rapid spread of community acquired methicillin resistant Staphylococcus aureus further highlights the threat of resistance development and illustrates the need for new antibiotics that work by novel mechanisms. 2 Given the broad genetic and physiological diversity of bacterial pathogens and the need for empiric therapies that cover a broad panel of organisms, it is not surprising that discovery of new antibiotics has advanced slowly. Central to antibiotic discovery is identifying broadly validated targets. One such proven target is the bacterial ribosome, which is the target for a significant number of clinically important antibiotics that bind at the ribosomal RNA (rRNA). 3 Here, we expand on the description of a novel series of antibacterial compounds that target rRNA and blocks bacterial translation and growth. 4Three-dimensional structures of different aminoglycosides bound to the decoding site, or Asite, within the 16S rRNA have been determined by X-ray crystallography. 5 Importantly, these studies have shown that 2-deoxystreptamine (2-DOS), a conserved core scaffold among aminoglycosides, binds in a similar manner regardless of the 4,5-or 4,6-disubstitutions found in the neomycin or gentamicin families, respectively (Fig. 1) Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript groups of 2-DOS are predominantly involved in base recognition by forming conserved hydrogen bonds with A1493, G1494 and U1495 of the 16S rRNA. These interactions anchor the aminoglycoside scaffold within the A-site internal loop and displace residues A1492 and A1493 from the RNA interior. These two adenine residues act as a molecular switch that is involved in securing the fidelity of translation by interacting w...
The widespread emergence of antibiotic-resistant bacteria and a lack of new pharmaceutical development have catalyzed a need for new and innovative approaches for antibiotic drug discovery. One bottleneck in antibiotic discovery is the lack of a rapid and comprehensive method to identify compound mode of action (MOA). Since a hallmark of antibiotic action is as an inhibitor of essential cellular targets and processes, we identify a set of 308 essential genes in the clinically important pathogen Staphylococcus aureus. A total of 446 strains differentially expressing these genes were constructed in a comprehensive platform of sensitized and resistant strains. A subset of strains allows either target underexpression or target overexpression by heterologous promoter replacements with a suite of tetracycline-regulatable promoters. A further subset of 236 antisense RNA-expressing clones allows knockdown expression of cognate targets. Knockdown expression confers selective antibiotic hypersensitivity, while target overexpression confers resistance. The antisense strains were configured into a TargetArray in which pools of sensitized strains were challenged in fitness tests. A rapid detection method measures strain responses toward antibiotics. The TargetArray antibiotic fitness test results show mechanistically informative biological fingerprints that allow MOA elucidation.
We report the structure-guided discovery, synthesis, and initial characterization of 3,5-diamino-piperidinyl triazines (DAPT), a novel translation inhibitor class that targets bacterial rRNA and exhibits broad-spectrum antibacterial activity. DAPT compounds were designed as structural mimetics of aminoglycoside antibiotics which bind to the bacterial ribosomal decoding site and thereby interfere with translational fidelity. We found that DAPT compounds bind to oligonucleotide models of decoding-site RNA, inhibit translation in vitro, and induce translation misincorporation in vivo, in agreement with a mechanism of action at the ribosomal decoding site. The novel DAPT antibacterials inhibit growth of gram-positive and gram-negative bacteria, including the respiratory pathogen Pseudomonas aeruginosa, and display low toxicity to human cell lines. In a mouse protection model, an advanced DAPT compound demonstrated efficacy against an Escherichia coli infection at a 50% protective dose of 2.4 mg/kg of body weight by single-dose intravenous administration.
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