STUDIES ON THE RIBOSOMES OF STREPTOMYCIN-SENSITIVE AND RESISTANT STRAINS OF ESCHERICHIA COLI

Observing mechanosensitive channels in action in living bacteria

Mechanosensitive (MS) channels act to protect the cytoplasmic membrane (CM) of living cells from environmental changes in osmolarity. In this report, we demonstrate the use of time-resolved second-harmonic light scattering (SHS) as a means of experimentally observing the relative state (open versus closed) of MS channels in living bacteria suspended in different buffer solutions. Specifically, the state of the MS channels was selectively controlled by changing the composition of the suspension medium, inducing either a transient or persistent osmotic shock. SHS was then used to monitor transport of the SHG-active cation, malachite green, across the bacterial CM. When MS channels were forced open, malachite green cations were able to cross the CM at a rate at least two orders of magnitude faster compared with when the MS channels were closed. These observations were corroborated using both numerical model simulations and complementary fluorescence experiments, in which the propensity for the CM impermeant cation, propidium, to stain cells was shown to be contingent upon the relative state of the MS channels (i.e., cells with open MS channels fluoresced red, cells with closed MS channels did not). Application of time-resolved SHS to experimentally distinguish MS channels opened via osmotic shock versus chemical activation, as well as a general comparison with the patch-clamp method is discussed.

Aminoglycoside Functionalization as a Tool for Targeting Nucleic Acids

Aminoglycoside functionalization as a tool for targeting natural and unnatural nucleic acids holds great promise in their development as diagnostic probes and medicinally relevant compounds. Simple synthetic procedures designed to easily and quickly manipulate amino sugar (neomycin, kanamycin) to more powerful and selective ligands are presented in this chapter. We describe representative procedures for (a) aminoglycoside conjugation and (b) preliminary screening for their nucleic acid binding and selectivity.

A nanovehicle developed for treating deep-seated bacteria using low-dose X-ray

Many non-antibiotic strategies, such as photocatalysis and photodynamic therapy, have been proposed to inhibit and/or kill bacteria. However, these approaches still have drawbacks such as insufficient bacterial specificity and the limited penetration depth of ultraviolet and near-infrared light. To overcome these limitations, we developed a bacteria-specific anti-bacterial technique via using low-dose X-ray. Graphene oxide quantum dots (GQDs, a multifunctional vehicle) conjugated with vancomycin (Van, a bacteria-targeting ligand) were assembled with Protoporphyrin IX (PpIX, a photo/radiation sensitizer) to yield a novel Van-GQDs/PpIX complex that specifically attached to Escherichia coli and efficiently generated intracellular reactive oxygen species following X-ray activation. Delivery using GQDs increased the PpIX/Van ratio in the target bacterial cell, damaged bacterial cell wall, and enhanced X-ray-induced PpIX activation. Hence, this approach allowed for the use of a low-dose X-ray to efficiently activate the Van-GQDs/PpIX complex to exert its bactericidal effects on Escherichia coli without damaging normal cells. Furthermore, the E. coli did not develop resistance to the proposed approach for at least 7 rounds of repeated administration during one week. Thus, this proposed vehicle exhibiting bacteria-specific X-ray-triggered toxicity is a promising alternative to antibiotics for treating serious bacterial infections occurring in deep-seated tissues/organs (e.g., osteomyelitis and peritonitis).

STATEMENTS OF SIGNIFICANCE

Administration of antibiotics is the most common treatment modality for bacterial infections. However, in some cases, patient attributes such as age, health, tolerance to antibiotics do not allow for the use of high-dose antibiotics. In addition, some bacteria develop resistance to antibiotics because of improper and long-term use of these agents. Therefore, non-antibiotic strategies to treat deeply situated bacterial infections, such as osteomyelitis, are urgently needed for avoiding amputation. To date, several non-antibiotic approaches, such as Ag nanoparticles, graphene-based materials, photocatalysis, and photodynamic therapy have been proposed to inhibit and/or kill bacteria. However, the major challenges of photochemical strategies, specificity and limited penetration depth of light source, still remain for treating the deep-seated bacteria. To overcome these problems, we developed a novel nanovehicle that exerted toxic effects specifically on bacteria following activation by a deeply penetrative low-dose X-ray, without damaging normal cells. As such, it realizes a deeply photochemical route for treating the deep-seated bacteria.

Biosynthetic Genes for the Tetrodecamycin Antibiotics

We recently described 13-deoxytetrodecamycin, a new member of the tetrodecamycin family of antibiotics. A defining feature of these molecules is the presence of a five-membered lactone called a tetronate ring. By sequencing the genome of a producer strain, Streptomyces sp. strain WAC04657, and searching for a gene previously implicated in tetronate ring formation, we identified the biosynthetic genes responsible for producing 13-deoxytetrodecamycin (the ted genes). Using the ted cluster in WAC04657 as a reference, we found related clusters in three other organisms: Streptomyces atroolivaceus ATCC 19725, Streptomyces globisporus NRRL B-2293, and Streptomyces sp. strain LaPpAH-202. Comparing the four clusters allowed us to identify the cluster boundaries. Genetic manipulation of the cluster confirmed the involvement of the ted genes in 13-deoxytetrodecamycin biosynthesis and revealed several additional molecules produced through the ted biosynthetic pathway, including tetrodecamycin, dihydrotetrodecamycin, and another, W5.9, a novel molecule. Comparison of the bioactivities of these four molecules suggests that they may act through the covalent modification of their target(s).

IMPORTANCE

The tetrodecamycins are a distinct subgroup of the tetronate family of secondary metabolites. Little is known about their biosynthesis or mechanisms of action, making them an attractive subject for investigation. In this paper we present the biosynthetic gene cluster for 13-deoxytetrodecamycin in Streptomyces sp. strain WAC04657. We identify related clusters in several other organisms and show that they produce related molecules.

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

The primary mechanism of action of the antibiotic dihydrostreptomycin is binding to and modifying the function of the bacterial ribosome, thus leading to decreased and aberrant translation of proteins; however, the routes by which it enters the bacterial cell are largely unknown. The mechanosensitive channel of large conductance, MscL, is found in the vast majority of bacterial species, where it serves as an emergency release valve rescuing the cell from sudden decreases in external osmolarity. While it is known that MscL expression increases the potency of dihydrostreptomycin, it has remained unclear if this effect is due to a direct interaction. Here, we use a combination of genetic screening, MD simulations, and biochemical and mutational approaches to determine if dihydrostreptomycin directly interacts with MscL. Our data strongly suggest that dihydrostreptomycin binds to a specific site on MscL and modifies its conformation, thus allowing the passage of K+ and glutamate out of, and dihydrostreptomycin into, the cell.

Gene Transfer in Mycobacterium tuberculosis: Shuttle Phasmids to Enlightenment

Infectious diseases have plagued humankind throughout history and have posed serious public health problems. Yet vaccines have eradicated smallpox and antibiotics have drastically decreased the mortality rate of many infectious agents. These remarkable successes in the control of infections came from knowing the causative agents of the diseases, followed by serendipitous discoveries of attenuated viruses and antibiotics. The discovery of DNA as genetic material and the understanding of how this information translates into specific phenotypes have changed the paradigm for developing new vaccines, drugs, and diagnostic tests. Knowledge of the mechanisms of immunity and mechanisms of action of drugs has led to new vaccines and new antimicrobial agents. The key to the acquisition of the knowledge of these mechanisms has been identifying the elemental causes (i.e., genes and their products) that mediate immunity and drug resistance. The identification of these genes is made possible by being able to transfer the genes or mutated forms of the genes into causative agents or surrogate hosts. Such an approach was limited in Mycobacterium tuberculosis by the difficulty of transferring genes or alleles into M. tuberculosis or a suitable surrogate mycobacterial host. The construction of shuttle phasmids-chimeric molecules that replicate in Escherichia coli as plasmids and in mycobacteria as mycobacteriophages-was instrumental in developing gene transfer systems for M. tuberculosis. This review will discuss M. tuberculosis genetic systems and their impact on tuberculosis research.

Sensitivity and Resistance to Spectinomycin in Escherichia coli

Inhibition of growth and division of Escherichia coli by spectinomycin is reversible, and the kinetics of its interference with deoxyribonucleic and ribonucleic acid synthesis may be interpreted as secondary effects of inhibition of protein synthesis on the ribosome. Spontaneous mutations to spectinomycin resistance occur in E. coli K-12 at a rate of about 2 x 10(-10). Resistance is transducible with a discrete lag in phenotypic expression, and the kinetics of its development is about the same as that for streptomycin resistance. All spectinomycin-resistant mutants tested contain resistant ribosomes, and all map in a locus (spc) counterclockwise to and 70% cotransducible with the classical str locus. Differences in the residual drug sensitivity of various spectinomycin-resistant mutants, and of their ribosomes, indicate the existence of more than one phenotypic class of resistance.

Gathering No Moss

I never imagined that I would be asked to write an autobiography in a microbiology tome. For that matter, little did I think that I would consider microbiology the most intriguing subject in the life sciences and the only field I wanted to study. My formal scientific training was in chemistry. This is a recounting of my conversion and the opportunities I have had to work in the microbial sciences with some of the major figures (and characters) during a period of marvelous intensity and productivity. I want to recognize and thank my many distinguished colleagues for the ways in which they have helped me to experience a fruitful and stimulating life as a microbiologist.

RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA

Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.

Experimental pneumococcus infection in mice: correlation of bactericidal activity in vitro with the effect in vivo for gentamicin, netilmicin and tobramycin

An experimental model in mice, incorporating the intraperitoneal inoculation of a Streptococcus pneumoniae type 3, was used to evaluate the effect in vivo after single-dose administration of the three aminoglycosides, gentamicin, tobramycin and netilmicin, and to correlate this effect with their in vitro activity against the pathogen, in particular the bactericidal rate. The minimal inhibitory concentrations (MIC's), which were equal to the minimal bactericidal concentrations (MBC's), were 12.5 micrograms/ml for netilmicin, and 25 micrograms/ml for the two other aminoglycosides, respectively. All three antibiotics showed excellent bactericidal activities even at concentrations 1/4 times the MIC's, but the bactericidal rate was clearly lower for tobramycin than for the two other aminoglycosides. The effect in vivo measured as the 50% effective dose (ED50) closely reflected the relative bactericidal activities of the drugs. Of the pharmacokinetic parameters investigated on dosages equal to the ED50's for the three drugs, the best to correlate with the bactericidal rates in vitro were the peak serum concentrations.

Gentamicin uptake in Staphylococcus aureus possessing plasmid-encoded, aminoglycoside-modifying enzymes

[3H]gentamicin uptake and killing were studied in three strains of gentamicin-resistant Staphylococcus aureus possessing plasmid-encoded, gentamicin-modifying enzymes and in three isogenic, enzyme-free, gentamicin-susceptible derivatives. At low (less than or equal to 2.0 micrograms/ml) concentrations of gentamicin, uptake by resistant organisms was impaired compared with that of susceptible strains, and no killing was noted. In contrast, at higher (2.5 to 10.0 micrograms/ml) concentrations (which were below the MIC for the resistant strains), rapid gentamicin uptake similar to that seen in susceptible isolates was observed. Although growth inhibition at these concentrations was apparent, there was no loss of viability in resistant strains. Consistently, the membrane H+-ATPase inhibitor N,N'-dicyclohexyl carbodiimide caused resistant strains to take up low concentrations (1.0 microgram/ml) of gentamicin at rates comparable to those seen in susceptible organisms without causing an associated loss of viability. These studies show differences between gentamicin uptake in S. aureus and streptomycin uptake in Escherichia coli (Dickie et al., Antimicrob. Agents Chemother. 14:569-580, 1978) regarding the kinetics of uptake in resistant strains with plasmid-encoded aminoglycoside-modifying enzymes. Specifically, they suggest that for 2-deoxystreptamine compounds such as gentamicin, ribosomal binding followed by accelerated uptake and subsequent interference with cell growth may occur without invariably being associated with lethal effect.

Tobramycin levels in aqueous humor after subconjunctival injection in humans

Subconjunctival injection of 10 mg of tobramycin provided therapeutic levels in the aqueous humor of 25 patients (ranging in age from 51 to 89 years) who underwent cataract surgery. The absorption from the subconjunctival tissue into the anterior chamber was fairly rapid, reaching a peak in approximately two hours. Peak levels were usually 20 times the minimum inhibitory concentration for Pseudomonas aeruginosa. The drug then gradually disappeared from the aqueous but still exceeded the minimum inhibitory concentration for Pseudomonas organisms after eight hours.

Search for ribosomal mutants in Podospora anserina: genetic analysis of mutants resistant to paromomycin

It has recently been shown that paromomycin, an antibiotic of the aminoglycoside family, is also active on eukaryotic cytoplasmic ribosomes. In the fungus Podospora anserina, genetic analysis of ten mutants resistant to high doses of paromomycin shows that this resistance is caused by mutations in two different nuclear genes. These mutants display pleiotropic phenotypes (cold sensitivity, mycelium and spore appearance and coloration, cross-resistance to other antibiotics). Double mutants are either lethal or very altered and unstable. Moreover, the cytochrome spectra of these mutants seem to indicate that cytoplasmic protein synthesis is affected. The mutants also display a slight suppressor effect. We can therefore assume that these mutations affect cytoplasmic ribosomes.

Viomycin favours the formation of 70S ribosome couples

The peptide antibiotic viomycin at a concentration of 10 muM inhibits E. coli ribosomes to the extent of about 70% as measured in the poly (U) system, and to about 85% in a natural mRNA (R17) system. Ribosomes from M. smegmatis show no activity at all at this concentration of the antibiotic. Experiments on the Mg+2 dependent dissociation and association of the ribosomal subunits revealed that viomycin stabilizes the 70S couples and promotes association of ribosomal subunits. This response is related to the drug action as indicated by the observation that viomycin resistant strains are not affected by viomycin with respect to dissociation and 70S couple information. A model for the inhibitory action of the drug is proposed.

A cycloheximide sensitivity factor from yeast required for N-acetylphenylalanylpuromycin formation

A protein (factor P) has been isolated from yeast, which was required for sensitivity to cycloheximide of a partially purified polyphenylalanine synthesis system. In the absence of factor P, 10(-3) M cycloheximide was required for 50% inhibition of polyphenylalanine synthesis, while in its presence, 10(-6) M gave 50% inhibition. Coincident with cycloheximide sensitivity was an activity required for EF-2 dependent N-acetylphenylalanylpuromycin (N-AcPhePuro) formation. Transfer of N-AcPhe to puromycin from the tRNA bound in the presence of 26 mM MgCl2 required factor P, as well as EF-2. Studies with antibody against EF-2 demonstrated that P factor was not required during the EF-2 translocation step but for some subsequent step.

Phenotypic instability in a tif-1 Mutant of Escherichia coli. I. Impairment in ribosomal function

The mutant T44(lambda) of Escherichia coli K12, grown in the presence of adenine, develops an increased tolerance to streptomycin. In cultures grown on streptomycin, the ts character (tif) may temporarily be suppressed but, on further transfer, both the temperature-sensitive phenotype and streptomycin tolerance disappear. In a cell-free system, the relative efficiency of translation of MS2 and poly U messenger RNAs was, respectively, 75 and 50% lower in extracts from cultures grown at 37 degrees with adenine than in extracts from 30 degrees cultures. Similar results were obtained when adenine was added in vitro to an extract from a culture grown at 37 degrees in the absence of adenine, using MS2 RNA as messenger. Moreover, the 37 degrees extracts showed a much lower misincorporation of isoleucine into polyphenylalanine in the poly U system. In addition, the Mg++ concentration required for optimal translational acitvity was higher for the 37 degrees than for the 30 degrees extracts. Extracts from a culture grown in L medium at 37 degrees or from a tif-/F'tif+ merodiploid grown at 37 degrees with adenine behaved similarly to that from the 30 degrees culture when poly U was used as messenger RNA. It is suggested that the tif+ gene product may play a regulatory role in ribosomal function and the pleiotropic nature of the tif-1 mutation could be due to impairment of translational activity augmented by elevated temperature or by adenine.

Nebramycin, a new broad-spectrum antibiotic complex. IV. In vitro and in vivo laboratory evaluation

In vivo treatment of susceptible Escherichia coli cultures with low concentrations of dihydrostreptomycin leads to a decline in polysomes and a corresponding increase in 70S particles which behave as run-off ribosomes, as well as free 30S and 50S subunits. We have examined the timing and extent of these effects on ribosomes and compared them to the effects of this antibiotic on growth and protein synthesis. We have shown that no changes in ribosome distribution are observed until growth inhibition by dihydrostreptomycin is almost complete. Thus, intracellular dihydrostreptomycin can inhibit growth and net protein synthesis without apparently affecting the ribosome cycle. Since it is known that the antibiotic combines with free 30S subunits, the question is how such combination can bring about the observed inhibition of protein synthesis and growth. We suggest that specific interaction of intracellular antibiotic with proteins of the 30S subunits allows repeated use of the ribosome cycle by such affected particles, but with selective misreading of certain amino acid codons as terminator codons, so that they produce incomplete polypeptide chains. The cumulative effect of such a mechanism would lead to eventual cessation of protein synthesis and growth.

Ribosomal resistance to streptomycin and spectinomycin in Neisseria gonorrhoeae

A cell-free protein synthesizing system was used to study the mechanism of resistance to streptomycin (Str) and spectinomycin (Spc) in laboratory mutants and clinical isolates of Neisseria gonorrhoeae. The 70S ribosomes from sensitive strains were sensitive to the effects of Str and Spc on synthesis directed by several synthetic polynucleotide messengers, whereas 70S ribosomes from resistant strains were resistant to these same effects. In each case, the alteration was localized to the 30S ribosomal subunit by studying antibiotic sensitivities of hybrid 70S ribosomes formed by combining subunits from sensitive and resistant strains. No evidence was found for streptomycin- or spectinomycin-inactivating enzymes.

Chloroplast and cytoplasmic ribosomes of Euglena: selective binding of dihydrostreptomycin to chloroplast ribosomes

Dihydrostreptomycin binds preferentially to chloroplast ribosomes of wild-type Euglena gracilis Klebs var. bacillaris Pringsheim. The K(diss) for the wild-type chloroplast ribosome-dihydrostreptomycin complex is 2 x 10(-7) M, a value comparable with that found for the Escherichia coli ribosome-dihydrostreptomycin complex. Chloroplast ribosomes isolated from the streptomycin-resistant mutant Sm(1) (r)BNgL and cytoplasmic ribosomes from wild-type have a much lower affinity for the antibiotic. The K(diss) for the chloroplast ribosome-dihydrostreptomycin complex of Sm(1) (r) is 387 x 10(-7) M, and the value for the cytoplasmic ribosome-dihydrostreptomycin complex of the wild type is 1,400 x 10(-7) M. Streptomycin competes with dihydrostreptomycin for the chloroplast ribosome binding site, and preincubation of streptomycin with hydroxylamine prevents the binding of streptomycin to the chloroplast ribosome. These results indicate that the inhibition of chloroplast development and replication in Euglena by streptomycin and dihydrostreptomycin is related to the specific inhibition of protein synthesis on the chloroplast ribosomes of Euglena.

Binding of dihydrostreptomycin to Escherichia coli ribosomes: characteristics and equilibrium of the reaction

The binding of dihydrostreptomycin to ribosomes and ribosomal subunits of a number of different Escherichia coli strains was studied, and the Mg(2+) and pH dependence, as well as the effect of salts and polynucleotides, was determined. The only requirement for binding with ribosomes and subunits from susceptible strains was 10 mm Mg(2+). Monovalent salts weakened the binding in a manner similar to the effects on ribonucleic acid secondary structure, and this was antagonized to some extent by increased amounts of Mg(2+). Bound dihydrostreptomycin could be readily exchanged by streptomycin and any antibiotically active derivative, but not by fragments of the antibiotic or any other aminoglycoside. With native (run-off) 70S ribosomes from streptomycin-susceptible strains, the binding was rapid and relatively temperature independent over the range from 0 to 37 C. Polynucleotides did not stimulate the binding. With concentrations of dihydrostreptomycin up to 10(-5)m, greater than 95% of native 70S ribosomes bound exactly 1 molecule of the antibiotic tightly, with a K(diss) for the bound complex at 25 C of 9.4 x 10(-8)m. The following thermodynamic parameters were found for the binding with 70S ribosomes at 25 C:DeltaG degrees = -9.6 kcal/mole, DeltaH degrees = -6.2 kcal/mole, and DeltaS degrees = +11.4 entropy units/mole. Differences in affinity for the antibiotic were found between ribosomes of K-12 strains and those of other E. coli strains. There was insignificant binding to 70S ribosomes or subunits from streptomycin-resistant or -dependent strains, and to 50S subunits from susceptible strains. The binding to 30S subunits from susceptible strains was weaker by an order of magnitude than that to the 70S particle, with a K(diss) at 25 C of 10(-6)m. Polyuridylic acid stimulated this binding slightly but did not influence the affinity of the bound molecule. At antibiotic concentrations above 10(-5)m, streptomycin-susceptible 70S and 30S particles bound additional molecules of the antibiotic, and binding also occurred to ribosomes from streptomycin-resistant and -dependent strains, as well as to 50S subunits from all strains. K(diss) for all of these binding equilibria were [Formula: see text] 10(-4)m. This weaker non-specific binding coincided with the beginning of aggregation phenomena involving the particles, and occurred at sites distinct from the single site which binds the antibiotic tightly. This latter site was completely lost after the one-step mutation to high-level resistance or dependence.

Analysis of ribosomes from viomycin-sensitive and -resistant strains of Mycobacterium smegmatis

Viomycin-resistant strains were isolated from Mycobacterium smegmatis. Ribosomes were isolated and tested for drug resistance in subcellular systems containing poly(U) as messenger ribonucleic acid. Resistance to viomycin in these strains was due to altered ribosomes. Further analysis showed that viomycin resistance of two mutants with low level resistance (20 mug/ml) was due to altered 30S ribosomal subunits. Another mutant that was highly resistant to viomycin (1 mg/ml), however, had altered 50S ribosomal subunits.

Mechanisms and spectrum of streptomycin resistance in a natural population of Pseudomonas aeruginosa

A survey of 200 strains of Pseudomonas aeruginosa isolated from clinical specimens was made in an attempt to correlate the spectrum of their streptomycin resistance and the mechanism of resistance. The strains can be classified into three groups, according to their level of resistance to streptomycin: susceptible, low-level resistant, and high-level resistant strains. The mechanism of resistance of high-level resistant strains is either an R factor-mediated inactivation of streptomycin by phosphorylation or streptomycin-resistant ribosomes. However, such high-level resistant strains comprised less than 10% of the total strains isolated; the majority of the strains resistant to streptomycin were of low-level resistance. The latter are associated with a diminished uptake of streptomycin, and no evidence of streptomycin inactivation, resistant ribosomes, or R factors could be detected. The most probable explanation of low-level resistance is reduced permeability to streptomycin. Modification of the growth medium used in uptake studies simultaneously affected strongly both streptomycin incorporation and the minimal inhibitory concentration of streptomycin.

Selection of ribosomal mutants by antibiotic suppression in yeast

Wild-type Saccharomyces cerevisiae is highly resistant to streptomycin. A histidine auxotroph was found which could grow without histidine in the presence of high concentrations of streptomycin. Selection for derivatives of this strain which could be suppressed by much lower concentrations of streptomycin yielded streptomycin-sensitive mutants which are cold-sensitive and have altered ribosomal profiles.