• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Curr Opin Chem Biol. Author manuscript; available in PMC Aug 1, 2009.
Published in final edited form as:
Curr Opin Chem Biol. Aug 2008; 12(4): 389–399.
Published online Jul 14, 2008. doi:  10.1016/j.cbpa.2008.06.015
PMCID: PMC2570263
NIHMSID: NIHMS70722

Exposing Plasmids as the Achilles’ Heel of Drug-Resistant Bacteria

Abstract

Many multi-drug resistant bacterial pathogens harbor large plasmids that encode proteins conferring resistance to antibiotics. While the acquisition of these plasmids often enables bacteria to survive in the presence of antibiotics, it is possible that plasmids also represent a vulnerability that can be exploited in tailored antibacterial therapy. This review highlights three recently described strategies designed to specifically combat bacteria harboring such plasmids: Inhibition of plasmid conjugation, inhibition of plasmid replication, and exploitation of plasmid-encoded toxin-antitoxin systems.

Introduction

Bacterial resistance to antibiotics is a worldwide health crisis [1]. Resistance to multiple antibiotics has been reported in nearly all pathogenic bacteria, with vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), multi-drug resistant (MDR) Pseudomonas aeruginosa, extensively-drug resistant (XDR) Mycobacterium tuberculosis, MDR Acinetobacter baumannii, β-lactam-resistant Enterobacteriaceae, and penicillin-resistant Streptococcus pneumoniae (PRSP) being particularly notorious [1-3]. Resistance typically occurs as a result of chromosomal mutation or acquisition of a mobile genetic element, such as a plasmid, that harbors resistance-mediating genes. The looming threat of a “post-antibiotic” era where untreatable bacterial infections are common is exacerbated by the shift of research programs in the pharmaceutical industry away from the development of novel antibacterials [4,5]. New strategies to combat drug-resistant bacteria are necessary to keep pace with ever-evolving bacterial resistance.

Plasmids as mobile genetic elements that mediate drug resistance

Lateral transfer of mobile genetic elements between diverse bacteria leads to a rapid dissemination of genes encoding resistance to antibiotics. These mobile genetic elements include plasmids, which are extrachromosomal DNA that transfer horizontally within and across bacterial genera and species by conjugation. Plasmids can also serve as vehicles for transposons and integrons; thus, through plasmid conjugation bacteria are exposed to a wide array of genes from the mobile gene pool. Plasmid-encoded resistance to multiple antibiotics, including β-lactams, aminoglycosides, tetracyclines, macrolides, and glycopeptides is prevalent in a plethora of pathogenic bacteria including VRE and MRSA [6,7]. In fact, recent analyses of >100 VRE isolates from humans, animals, and food show that vanA, the gene cluster encoding vancomycin resistance, resides in the Tn1546 transposon carried on plasmids [8,9]. In addition, plasmid-encoded virulence and antibiotic resistance contribute to the pathogenicity of biowarfare agents such as Bacillus anthracis and Yersinia pestis [10-12]. Most frightening is the recently observed transfer of plasmids from VRE to MRSA, resulting in the virtually untreatable vancomycin resistant S. aureus (VRSA) [13,14].

However, the very nature of their importance to the antibiotic resistant phenotype may expose plasmids as the Achilles’ heel of drug-resistant bacteria. Indeed, creative strategies have recently been devised to prevent the transfer of plasmids between bacteria, to inhibit plasmid replication and hence induce the elimination of plasmids from bacteria, and to exploit plasmid maintenance systems to directly and selectively induce death in drug-resistant bacteria (Figure 1). [15-24]. Although compounds based on these approaches have not yet progressed to clinical trials, the well-documented prevalence of plasmids within the most problematic drug-resistant bacteria makes the targeting of plasmid-encoded elements an intriguing antibacterial option. This Current Opinion focuses on these recent efforts to exploit plasmids in antibacterial therapy.

Fig. 1
Three approaches to exploit plasmids in antibacterial therapy. 1. Plasmids are transferred between bacteria through conjugation. Inhibition of the relaxase enzyme (blue oval) has been proposed as an antibacterial strategy, and several relaxase inhibitors ...

Inhibition of plasmid conjugation

To prevent the transfer and dissemination of resistance-mediating plasmids, the inhibition of plasmid conjugation has been postulated as a prophylactic strategy [15,25]. Using a cell-based assay involving the transfer of a plasmid containing the lux gene (encoding luciferase) from a donor strain to a recipient strain (Figure 2A), chemical libraries and bacterial/fungal extracts were screened for inhibitors of plasmid conjugation [15,16]. Through these screens dehydrocrepenynic acid (DHCA) and linoleic acid were identified as conjugation inhibitors (Figure 2B). The compounds depicted in Figure 2B were found to only inhibit the transfer of plasmids with similar DNA replication and transfer machinery and did not inhibit the proteins involved in the mating bridge (mating pair formation). Secondary assays ruled out general inhibitory effects of these unsaturated fatty acids, suggesting that these compounds may act through a conjugation-specific mechanism [15].

Fig. 2
The identification of inhibitors of plasmid conjugation. (A) To screen for inhibitors of plasmid conjugation, a donor cell harboring an F plasmid derivative with the lux gene under control of the lac promoter is utilized. This cell also harbors a second ...

A subsequent study on conjugation inhibition also used the same fluorometric, cell-based assay to identify intrabodies that specifically inhibit conjugation [16]. Intrabodies are intracellularly-expressed antibodies that have been used to inactivate proteins in yeast [26,27], plants [28,29], mammals [30-32], and bacteria [33-35]. The relaxase enzyme, which catalyzes the cleaving and religating of plasmid DNA, is an essential component of plasmid conjugation systems (Figure 3A). Recognizing the critical importance of relaxases to plasmid conjugation, Garcillan-Barcia and co-workers expressed intrabodies in the recipient cell to inactivate the TrwC relaxase enzyme encoded by plasmid R388 in a proof-of-concept study [16]. Mice were immunized with the TrwC relaxase domain (the N-terminal 293 amino acids (N293)), and single chain Fv antibody clone libraries were created from splenocytes. Screening of the intrabody libraries for their binding to TrwC-N293 and for their inhibition of conjugation using the aforementioned fluorescence-based assay yielded two conjugation inhibitors, scFv-P4.E7 and scFv-P1.F2. Whereas scFv-P4.E7 recognizes a region of TrwC not known to be involved in catalysis, scFv-P1.F2 binds to the conserved motif 1 of the MOBF relaxase family, which is a mobile loop containing the catalytic tyrosine-26 [36,37]. TrwC relaxase function depends on two catalytic tyrosines: Y18 carries out the initial cleavage event at oriT and Y26 is thought to catalyze a transesterification, which recircularizes the T-DNA, the DNA that is transferred, in the recipient cell [38]. The observed 20-fold conjugation inhibition of scFv-P1.F2 matches the reduction in activity observed by the TrwC-Y26F mutant [38], suggesting that the binding of scFv-P1.F2 to the mobile Y26-containing loop may prevent the transesterification and recircularization of T-DNA in the recipient cell. Another intriguing result is that mutant TrwC-Y18F but not wild-type TrwC could partially rescue the reduced conjugation of TrwC-Y26F, suggesting different roles for each tyrosine and possible different conformations of TrwC during conjugative DNA processing. Using a target-based approach to study conjugation, these results confirm previous evidence that TrwC is active in the recipient cell and suggests relaxase inhibition is a viable strategy for preventing plasmid conjugation. However, because these intrabodies do not actually induce cell death, this type of prophylactic strategy would only be useful for preventing the dissemination of genes that mediate antibiotic resistance.

Fig. 3
Targeting relaxase as a strategy to inhibit plasmid conjugation. (A) Overview of the relaxase mechanism. The relaxase domain (shown as the blue circle) domain of TrwC binds the oriT (1) of the T-strand. Tyrosine-19 (shown as an orange circle) of relaxase ...

Although the use of relaxase-targeting intrabodies validated the notion that interference with relaxase function could inhibit plasmid conjugation, the therapeutic application of intrabodies will be difficult due to the biological stability, cell permeability, and pharmacokinetic problems faced by any macromolecular drug. In a recent study by Lujan and co-workers, however, a series of small molecule relaxase inhibitors were identified and shown to prevent plasmid conjugation [17]. Through X-ray crystallographic analysis of the F plasmid TraI-N300 relaxase domain, it was hypothesized that simple bisphosphonates could interact with the active site Mg2+ ion and two catalytic tyrosine residues to inhibit relaxase. Thus, an enzymatic assay was developed that measured the relaxase-catalyzed cleavage of a fluoroescently-labeled ssDNA containing the F plasmid oriT sequence. This assay showed that nanomolar concentrations of imidobisphosphate (PNP) (Figure 3B) inhibited relaxase-catalyzed cleavage of oriT ssDNA. The crystal structure of PNP-bound relaxase revealed a phosphate of PNP within 3.7 Å of the Mg2+ metal center. Of twelve bisphosphonates tested in the kinetic assay, six compounds (shown in Figure 3B) were found to potently inhibit relaxase.

A conventional conjugation assay showed that PNP inhibited transfer of the F plasmid between two E. coli cells with an EC50 of 10 μM. Surprisingly, PNP was found to selectively kill F+ E. coli expressing the TraI relaxase but had no effect on strains containing TraI relaxase but no F plasmid, F plasmid but no TraI relaxase, or F plasmid in which all four relaxase active site tyrosines were mutated to phenylalanines. These data suggests that PNP inhibits conjugation and produces a bactericidal effect dependent on the presence of active relaxase and F plasmid. The exact mechanism behind this relaxase-dependent antibacterial activity of bisphosphonates is unknown. All six bisphosphonates in Figure 3B inhibited conjugation and displayed F plasmid specific killing in the nanomolar-to-low-micromolar range, making them significantly more selective over cells lacking the F plasmid. Two of these potent bisphosphonates, Clodronate and Etidronate, are clinically approved for the treatment of bone disease. These compounds are promising candidates for use in combination with current antibiotics to prevent dissemination of plasmid-encoded antibiotic resistance in the gastrointestinal tract, and may have potential as single entity antibacterial agents against bacteria harboring plasmid-encoded relaxases. Before either of the relaxase-targeting strategies described above can be broadly utilized, there will need to be a demonstration that homologous relaxases are present and active in clinically significant bacterial pathogens.

Inhibition of plasmid replication by mimicking plasmid incompatibility

Another novel approach to combat bacteria harboring plasmid-encoded resistance genes is the use of small molecules to inhibit plasmid replication and hence eliminate the plasmid from the bacterial population. Plasmid incompatibility is a natural phenomenon for plasmid elimination; two plasmids of the same incompatibility group will not stably cosegregate to a daughter cell. Studies by DeNap et al. [18] and Thomas et al. [19] exploit this natural mechanism in the identification of small molecule mimics of plasmid incompatibility, “antiplasmid” compounds that eliminate plasmids from the bacterial population and re-sensitize the bacteria to antibiotics.

Plasmid incompatibility is determined by the plasmid replication machinery, which has been extensively studied in the incompatibility group B (IncB) plasmids [39-46]. IncB plasmid replication is tightly controlled by the levels of the phophodiesterase RepA [47,48], the translation of which is controlled by a small, untranslated RNA, called RNA I (Figure 4A). RepA mRNA forms an intramolecular pseudoknot between stem-loop I (SLI) and stem-loop III (SLIII), which allows RepA translation and hence plasmid replication [43]. RepA translation is shut down when the countertranscript RNA I binds SLI [39,44-46]. In an effort to mimic this process with a small molecule, antiplasmid compounds that bound to SLI were sought. A variety of aminoglycosides were tested for their ability to bind SLI RNA, and apramycin (Figure 4B) was found to bind with a Kd of 93 nM. Through mutagenesis studies it was determined that bases A22 and A23 on SLI were essential for apramycin binding, as this binding event was completely abolished in the SLI-A22G/A23G double mutant. Plasmid stability assays showed that the IncB plasmid was almost completely eliminated after 250 generations, and a general correlation between SLI binding affinity and plasmid loss was observed [19]. In contrast, when the SLI-A22G/A23G mutations were created on the same IncB plasmid (abolishing the apramycin binding site), this plasmid was not eliminated by apramycin. These studies demonstrate that plasmids can be eliminated from bacterial cells in a mechanistically distinct fashion, that is, through the identification of compounds that bind tightly to RNAs essential to plasmid replication control. For this approach to find clinical utility, the homology of the RNAs that mediate plasmid replication control in pathogenic bacteria will need to be investigated. The little information that is available does indicate that some plasmids do indeed have homologous regions in these key countertranscript RNAs [49,50]. Furthermore, identification of compounds that cause more rapid plasmid loss will improve this strategy and increase its potential in antibacterial therapy.

Fig 4
“Antiplasmid” antibiotics induce plasmid elimination from the bacterial cell population, resensitzing bacteria to antibiotics. A) Plasmid replication control by RepA. In IncB systems, an intramolecular pseudoknot forms between SLI and ...

Toxin-antitoxin systems

Proteic toxin-antitoxin systems, found on both bacterial plasmids and chromosomes, produce a stable toxic protein and a labile antitoxin protein. The possibility of exploiting toxin-antitoxin (TA) systems as a novel antibacterial strategy with a compound that activates the latent toxin through one of two pathways (Figure 5), has been proposed [6,20-22,51]; although the end result (toxin-induced cell death) is the same, the two strategies depicted in Figure 5 differ mechanistically. In pathway 1, a compound acts at either the transcriptional or translational level to prevent the synthesis of new antitoxin. Thus, when the highly labile pre-existing antitoxin molecules are degraded, the stable toxin is freed to kill the cell. The second mechanism for the exploitation of TA systems as antibacterial targets involves the direct disruption of the toxin-antitoxin protein-protein interaction, freeing the toxin to induce cell death (pathway 2 in Figure 5) [6,20,21,51]. When considering TA systems as an antibacterial target, it is helpful to make a distinction between TA systems found on chromosomes and those found on plasmids, although compounds acting through either mechanism should be effective against plasmid- and chromosomally-encoded TA systems alike.

Fig. 5
Activation of the toxin of a toxin-antitoxin system, and subsequent cell death. At least two mechanisms for toxin activation are possible. In pathway 1 (left), the small molecule acts to directly or indirectly to inhibit transcription and/or translation ...

Chromosomally-encoded toxin-antitoxin systems

Although the genes for toxin-antitoxin proteins have been found on bacterial and archaeal chromosomes, the function of chromosomally-encoded TA systems remains elusive. Data from several studies indicate that these systems function to halt bacterial growth during times of stress (Figure 6A). For example, the mazEF TA system has been described as a suicide module that causes programmed cell death (PCD) in response to extreme amino acid starvation. In this scenario relA synthesizes the stringent response molecule guanosine 3′,5′-bispyrophosphate (ppGpp), inhibiting mazEF transcription, activating MazF, and ultimately leading to cell death [52-54]. Furthermore, addition of antibacterials that inhibit transcription (rifampicin), translation (chloramphenicol and spectinomycin) or that cause thymine starvation (trimethoprim and sulfonamide) cause mazEF-dependent cell death [23,55,56]. Based on these studies it has been proposed that a new class of antibacterials could be developed that would stress the cells such that the toxin protein(s) are activated, causing cell death [22,23]. The recent discovery of a short peptide that appears to induce bacterial cell death in a MazF-dependent fashion in E. coli bolsters the argument that chromosomally-encoded TA systems are a tractable antibacterial target [24,57].

Fig. 6
The genes for toxin-antitoxin systems have different functions, depending on their location. A) Chromosomally-encoded TA systems are possibly used by the cell to respond to stress. Stress causes toxin activation and reversible inhibition of cell growth; ...

However, other studies offer conflicting evidence, including a recent report in which the genes for several chromosomally-encoded TA systems were systematically knocked out in E. coli, and the resulting bacterial strain had no obvious change in phenotype in response to the cellular stresses that were tested [58]. Given this contradictory evidence, a variety of potential functions for chromosomally-encoded TA systems have been postulated, including the possibility that they have no function [59]. TA systems have also been reported as modulators of the persister cell phenotype, in which cells neither grow nor die in the presence of bactericidal antibiotics, resulting in multi-drug tolerance (MDT) [60-62]. HipA, of the TA operon hipBA, was the first validated persister-MDT protein; knocking out hipA significantly reduces the occurrence of persister cells [61]. However, knocking out other TA systems shown to be involved in producing the persister cells in E. coli resulted in no phenotype, thus suggesting that persister genes are redundant [62].

Although several genomic studies have revealed the presence of TA genes on the chromosomes of a variety of different bacteria [63-65] and their absence in obligate host-associated organisms, definitive evidence showing that chromosomally-encoded TA genes are functional in clinical isolates of pathogenic bacteria will be required before disruption of chromosomally-encoded TA systems can be considered a viable antibacterial strategy. Furthermore, understanding the role of chromosomally-encoded TA systems in the formation of persister cells will help to further evaluate TA systems as an antibacterial target.

Plasmid-encoded toxin-antitoxin systems

The role of plasmid-encoded TA systems is to function as post-segregational killers (PSKs) (Figure 6B) [66-68]. Proteic TA systems are utilized by plasmids to ensure that only those daughter cells that inherit the plasmid survive after cell division. When both proteins are present, the antitoxin binds to the toxin, preventing its toxic activity. However, if during cell division a plasmid-free daughter cell arises, the labile antitoxin is quickly degraded (and not replenished), freeing the toxin to induce cell death. Because of this indelible link between plasmid maintenance and bacterial life, TA systems have been termed ‘plasmid addiction systems’ [69].

Before the search for toxin activators could commence, it was necessary to know if the genes for TA systems were present on plasmids isolated from major drug-resistant bacterial pathogens, if a certain TA systems was more prevalent than others (making it a more attractive antibacterial target), and if these plasmid-encoded TA genes were functional in the drug-resistant bacteria. A recent epidemiological survey of VRE isolates provided answers to these questions [21]. In this survey, plasmids were purified from 75 different VRE clinical isolates, and then probed by PCR for the presence of TA genes. Surprisingly, the genes for TA systems were found to be ubiquitous on plasmids from VRE and physically linked to the vanA gene cluster; 75 out of 75 VRE isolates contained plasmids harboring genes for TA systems. Certain TA systems were indeed more prevalent than others, with mazEF (75 out of 75), axe-txe (56 out of 75), relBE (35 out of 75), and ω-ε-ζ (33 out of 75) being the most common. RT-PCR showed that the mazEF transcripts are produced in the VRE isolates. Furthermore, plasmid pS345RF, which contains mazEF as the only detectable TA system, was shown to be highly stable in the absence of selection. Finally, the cloning of mazEF and its native promoter into the unstable enterococcal vector pAM401 was shown to impart a significant increase in plasmid stability, thus suggesting that TA systems are functional in VRE [21].

Targeting toxin-antitoxin systems

The discovery that certain TA systems are ubiquitous in clinical isolates of difficult-to-treat drug-resistant pathogens suggests the exciting possibility that disruption of TA systems could be a viable target for tailored antibacterial therapy. The next challenge is to develop high-throughput screens and use them to identify compounds that induce toxin-dependent death. In this vein, a continuous fluorometric assay that follows the ribonuclease activity of MazF was recently developed [70]. This assay employs a short oligonucleotide containing the MazF cleavage sequence 5′-labeled with 6-carboxyfluorescein (6-FAM) and 3′-labeled with a black-hole quencher (BHQI). Cleavage of the oligonucleotide releases the fluorophore from the quencher, resulting in a large increase in fluorescence emission of 6-FAM. This in vitro assay could be used to screen compounds for their ability to induce activation of MazF activity from the MazE-MazF complex. Cell-based assays to identify compounds that selectively restrict growth of toxin-antitoxin producing bacteria can also be envisioned.

It is possible that targeting plasmid-encoded TA systems could have advantages over traditional antibiotics. One could envision resistance to such toxin-activating compounds arising through an inactivating mutation in the toxin protein, or through mutation of the target of the toxic protein. However, both situations are problematic from the bacteria’s perspective. If the toxin protein is mutated and inactivated, a compound that released the toxin would indeed no longer be an effective antibacterial. On the other hand, this mutation would also eradicate the plasmid stabilization system, and hence the plasmid (containing the drug-resistance genes) would be eliminated from the bacterial population, re-sensitizing the bacteria to conventional antibiotics. Mutation of the target would be equally complicated as a resistance mechanism. It is difficult to foresee how toxic RNase activity (such as in MazF) could be abolished through target mutation. For the toxins that inhibit DNA gyrase (such as CcdB), mutants of this enzyme could indeed arise that are resistant to the toxin proteins. However, once again this sort of mutation would eliminate the natural function of the TA systems, that of plasmid stabilization; gyrase mutants would be resistant to the post-segregational killing effect, and plasmid-free daughter cells (that are sensitive to the effect of antibiotics) would likely arise quickly.

Analysis, Summary, and Future Directions

The very fact that plasmids are responsible for large swaths of drug-resistance in bacteria makes them attractive antibacterial targets. It would seem that prophylactic strategies, for example those that are designed to stop the spread of drug-resistance genes through inhibition of plasmid conjugation, are less attractive and less practical then those that directly induce bacteria cell death. However, as shown by the creative work of Lujan and co-workers [17], the prevention of plasmid conjugation through the inhibition of relaxase can indeed directly induce cell death, a surprising and welcome discovery. While strategies that rely on compounds to induce plasmid elimination may have some utility, the heterogeneity of the plasmid replication elements and the number of generations required for elimination will need to be defined in clinical isolates before this approach can be implemented. The direct induction of cell death through the disruption of toxin-antitoxin systems appears to hold considerable promise, given the ubiquity of certain TA systems on plasmids isolated from VRE and the strong toxicity of the various toxic proteins. Although the lack of plasmids in XDR M. tuberculosis presents a limitation for the proposed plasmid conjugation and replication inhibition antibacterial strategies, toxin-antitoxin systems have been shown to reside on the M. tuberculosis chromosome [63,71].

As these approaches toward utilizing mobile genetic elements against bacteria are further explored and exploited, a major effort will need to be made to move studies past proof-of-concept work in E. coli with model plasmids and into demonstrations in actual clinical isolates. Given the wide array of naturally occurring plasmids, target heterogeneity will be a major question for any strategy seeking to exploit a plasmid-encoded trait; an ideal target would be one that is fully conserved throughout a variety of difficult-to-treat bacteria. Because plasmids often harbor the genes for resistance-mediating enzymes, standard mechanisms of resistance may not be as applicable to compounds that target plasmid-encoded elements. Just as dipping Achilles into the river Styx gave him overall strength but left his heel vulnerable, so too does the very resistance conferred on bacteria by a plasmid make them susceptible to plasmid-targeting strategies.

Acknowledgements

The authors are grateful to the National Institutes of Health (NIHGMS R01-GM68385) and the Office of Naval Research (N00014-02-1-0390) for supporting research in the area of novel antibacterial strategies.

Footnotes

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.

References and recommended reading

• of special interest

•• of outstanding interest

1. Spellberg B, Guidos R, Gilbert D, Bradley J, Boucher HW, Scheld WM, Bartlett JG, Edwards J., Jr. The epidemic of antibiotic-resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin Infect Dis. 2008;46:155–164. [PubMed]
2. Alekshun MN, Levy SB. Molecular mechanisms of antibacterial multidrug resistance. Cell. 2007;128:1037–1050. [PubMed]
3. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5:175–186. [PubMed]
4. Alanis AJ. Resistance to antibiotics: are we in the post-antibiotic era? Arch Med Res. 2005;36:697–705. [PubMed]
5. Projan SJ. Why is big Pharma getting out of antibacterial drug discovery? Curr Opin Microbiol. 2003;6:427–430. [PubMed]
6. Moritz EM, Hergenrother PJ, Amabile-Ceuvas CF. Antimicrobial Resistance in Bacteria. Horizon Scientific Press; 2007. The Prevalence of Plasmids and Other Mobile Genetic Elements in Clinically Important Drug-resistant Bacteria; pp. 25–53.
7. Tenover FC, McDougal LK, Goering RV, Killgore G, Projan SJ, Patel JB, Dunman PM. Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States. J Clin Microbiol. 2006;44:108–118. [PMC free article] [PubMed]
8. Biavasco F, Foglia G, Paoletti C, Zandri G, Magi G, Guaglianone E, Sundsfjord A, Pruzzo C, Donelli G, Facinelli B. VanA-type enterococci from humans, animals, and food: species distribution, population structure, Tn1546 typing and location, and virulence determinants. Appl Environ Microbiol. 2007;73:3307–3319. [PMC free article] [PubMed]
9. Zheng B, Tomita H, Xiao YH, Wang S, Li Y, Ike Y. Molecular characterization of vancomycin-resistant enterococcus faecium isolates from mainland China. J Clin Microbiol. 2007;45:2813–2818. [PMC free article] [PubMed]
10. Okinaka RT, Cloud K, Hampton O, Hoffmaster AR, Hill KK, Keim P, Koehler TM, Lamke G, Kumano S, Mahillon J, et al. Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol. 1999;181:6509–6515. [PMC free article] [PubMed]
11. Luna VA, King DS, Peak KK, Reeves F, Heberlein-Larson L, Veguilla W, Heller L, Duncan KE, Cannons AC, Amuso P, et al. Bacillus anthracis virulent plasmid pX02 genes found in large plasmids of two other Bacillus species. J Clin Microbiol. 2006;44:2367–2377. [PMC free article] [PubMed]
12. Guiyoule A, Gerbaud G, Buchrieser C, Galimand M, Rahalison L, Chanteau S, Courvalin P, Carniel E. Transferable plasmid-mediated resistance to streptomycin in a clinical isolate of Yersinia pestis. Emerg Infect Dis. 2001;7:43–48. [PMC free article] [PubMed]
13. Weigel LM, Clewell DB, Gill SR, Clark NC, McDougal LK, Flannagan SE, Kolonay JF, Shetty J, Killgore GE, Tenover FC. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science. 2003;302:1569–1571. [PubMed]
14. Weigel LM, Donlan RM, Shin DH, Jensen B, Clark NC, McDougal LK, Zhu W, Musser KA, Thompson J, Kohlerschmidt D, et al. High-Level Vancomycin-Resistant Staphylococcus aureus Isolates Associated with a Polymicrobial Biofilm. Antimicrob. Agents Chemother. 2007;51:231–238. [PMC free article] [PubMed]
15. Fernandez-Lopez R, Machon C, Longshaw CM, Martin S, Molin S, Zechner EL, Espinosa M, Lanka E, de la Cruz F. Unsaturated fatty acids are inhibitors of bacterial conjugation. Microbiology. 2005;151:3517–3526. [PubMed]
16. Garcillan-Barcia MP, Jurado P, Gonzalez-Perez B, Moncalian G, Fernandez LA, de la Cruz F. Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies. Mol Microbiol. 2007;63:404–416. [PubMed]
17. Lujan SA, Guogas LM, Ragonese H, Matson SW, Redinbo MR. Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A. 2007;104:12282–12287. [PMC free article] [PubMed]
18. DeNap JC, Thomas JR, Musk DJ, Hergenrother PJ. Combating drug-resistant bacteria: small molecule mimics of plasmid incompatibility as antiplasmid compounds. J Am Chem Soc. 2004;126:15402–15404. [PubMed]
19. Thomas JR, DeNap JC, Wong ML, Hergenrother PJ. The relationship between aminoglycosides’ RNA binding proclivity and their antiplasmid effect on an IncB plasmid. Biochemistry. 2005;44:6800–6808. [PubMed]
20. DeNap JC, Hergenrother PJ. Bacterial death comes full circle: targeting plasmid replication in drug-resistant bacteria. Org Biomol Chem. 2005;3:959–966. [PubMed]
21. Moritz EM, Hergenrother PJ. Toxin-antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci. Proc Natl Acad Sci U S A. 2007;104:311–316. [PMC free article] [PubMed]
22. Engelberg-Kulka H, Sat B, Reches M, Amitai S, Hazan R. Bacterial programmed cell death systems as targets for antibiotics. Trends Microbiol. 2004;12:66–71. [PubMed]
23. Engelberg-Kulka HS, Boaz, Hazan Ronen. Bacterial Programmed Cell Death and Antibiotics. ASM News. 2001;67:617–624.
24. Kolodkin-Gal I, Hazan R, Gaathon A, Carmeli S, Engelberg-Kulka H. A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science. 2007;318:652–655. [PubMed]
25. Smith PA, Romesberg FE. Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nat Chem Biol. 2007;3:549–556. [PubMed]
26. Carlson JR. A new means of inducibly inactivating a cellular protein. Mol Cell Biol. 1988;8:2638–2646. [PMC free article] [PubMed]
27. Visintin M, Tse E, Axelson H, Rabbitts TH, Cattaneo A. Selection of antibodies for intracellular function using a two-hybrid in vivo system. Proc Natl Acad Sci U S A. 1999;96:11723–11728. [PMC free article] [PubMed]
28. Tavladoraki P, Benvenuto E, Trinca S, De Martinis D, Cattaneo A, Galeffi P. Transgenic plants expressing a functional single-chain Fv antibody are specifically protected from virus attack. Nature. 1993;366:469–472. [PubMed]
29. Jobling SA, Jarman C, Teh MM, Holmberg N, Blake C, Verhoeyen ME. Immunomodulation of enzyme function in plants by single-domain antibody fragments. Nat Biotechnol. 2003;21:77–80. [PubMed]
30. Biocca S, Pierandrei-Amaldi P, Cattaneo A. Intracellular expression of anti-p21ras single chain Fv fragments inhibits meiotic maturation of xenopus oocytes. Biochem Biophys Res Commun. 1993;197:422–427. [PubMed]
31. Rondon IJ, Marasco WA. Intracellular antibodies (intrabodies) for gene therapy of infectious diseases. Annu Rev Microbiol. 1997;51:257–283. [PubMed]
32. Lobato MN, Rabbitts TH. Intracellular antibodies as specific reagents for functional ablation: future therapeutic molecules. Curr Mol Med. 2004;4:519–528. [PubMed]
33. Jurado P, Ritz D, Beckwith J, de Lorenzo V, Fernandez LA. Production of functional single-chain Fv antibodies in the cytoplasm of Escherichia coli. J Mol Biol. 2002;320:1–10. [PubMed]
34. Jurado P, de Lorenzo V, Fernandez LA. Thioredoxin fusions increase folding of single chain Fv antibodies in the cytoplasm of Escherichia coli: evidence that chaperone activity is the prime effect of thioredoxin. J Mol Biol. 2006;357:49–61. [PubMed]
35. Hu X, O’Hara L, White S, Magner E, Kane M, Wall JG. Optimisation of production of a domoic acid-binding scFv antibody fragment in Escherichia coli using molecular chaperones and functional immobilisation on a mesoporous silicate support. Protein Expr Purif. 2007;52:194–201. [PubMed]
36. Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat Struct Biol. 2003;10:1002–1010. [PubMed]
37. Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F. Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J Mol Biol. 2006;358:857–869. [PubMed]
38. Grandoso G, Avila P, Cayon A, Hernando MA, Llosa M, de la Cruz F. Two active-site tyrosyl residues of protein TrwC act sequentially at the origin of transfer during plasmid R388 conjugation. J Mol Biol. 2000;295:1163–1172. [PubMed]
39. Praszkier J, Bird P, Nikoletti S, Pittard J. Role of countertranscript RNA in the copy number control system of an IncB miniplasmid. J Bacteriol. 1989;171:5056–5064. [PMC free article] [PubMed]
40. Praszkier J, Wei T, Siemering K, Pittard J. Comparative analysis of the replication regions of IncB, IncK, and IncZ plasmids. J Bacteriol. 1991;173:2393–2397. [PMC free article] [PubMed]
41. Praszkier J, Wilson IW, Pittard AJ. Mutations affecting translational coupling between the rep genes of an IncB miniplasmid. J Bacteriol. 1992;174:2376–2383. [PMC free article] [PubMed]
42. Praszkier J, Pittard AJ. Role of CIS in replication of an IncB plasmid. J Bacteriol. 1999;181:2765–2772. [PMC free article] [PubMed]
43. Praszkier J, Murthy S, Pittard AJ. Effect of CIS on activity in trans of the replication initiator protein of an IncB plasmid. J Bacteriol. 2000;182:3972–3980. [PMC free article] [PubMed]
44. Praszkier J, Pittard AJ. Pseudoknot-dependent translational coupling in repBA genes of the IncB plasmid pMU720 involves reinitiation. J Bacteriol. 2002;184:5772–5780. [PMC free article] [PubMed]
45. Siemering KR, Praszkier J, Pittard AJ. Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication. J Bacteriol. 1993;175:2895–2906. [PMC free article] [PubMed]
46. Siemering KR, Praszkier J, Pittard AJ. Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication. J Bacteriol. 1994;176:2677–2688. [PMC free article] [PubMed]
47. Betteridge T, Yang J, Pittard AJ, Praszkier J. Interaction of the initiator protein of an IncB plasmid with its origin of DNA replication. J Bacteriol. 2003;185:2210–2218. [PMC free article] [PubMed]
48. Betteridge T, Yang J, Pittard AJ, Praszkier J. Role of RepA and DnaA proteins in the opening of the origin of DNA replication of an IncB plasmid. J Bacteriol. 2004;186:3785–3793. [PMC free article] [PubMed]
49. Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J Mol Biol. 1999;294:1115–1125. [PubMed]
50. Franch T, Gerdes K. U-turns and regulatory RNAs. Curr Opin Microbiol. 2000;3:159–164. [PubMed]
51. Gerdes K, Christensen SK, Lobner-Olesen A. Prokaryotic toxin-antitoxin stress response loci. Nat Rev Microbiol. 2005;3:371–382. [PubMed]
52. Aizenman E, Engelberg-Kulka H, Glaser G. An Escherichia coli chromosomal “addiction module” regulated by guanosine [corrected] 3′,5′-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci U S A. 1996;93:6059–6063. [PMC free article] [PubMed]
53. Engelberg-Kulka H, Reches M, Narasimhan S, Schoulaker-Schwarz R, Klemes Y, Aizenman E, Glaser G. rexB of bacteriophage lambda is an anti-cell death gene. Proc Natl Acad Sci U S A. 1998;95:15481–15486. [PMC free article] [PubMed]
54. Christensen SK, Pedersen K, Hansen FG, Gerdes K. Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J Mol Biol. 2003;332:809–819. [PubMed]
55. Sat B, Hazan R, Fisher T, Khaner H, Glaser G, Engelberg-Kulka H. Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality. J Bacteriol. 2001;183:2041–2045. [PMC free article] [PubMed]
56. Sat B, Reches M, Engelberg-Kulka H. The Escherichia coli mazEF suicide module mediates thymineless death. J Bacteriol. 2003;185:1803–1807. [PMC free article] [PubMed]
57. Kolodkin-Gal IE-K,H. The Extra-cellular Death Factor (EDF): Physiological and genetic factors influencing its production and response in Escherichia coli. J Bacteriol. 2008 In press, published ahead of print on February 29, 2008. [PMC free article] [PubMed]
58. Tsilibaris V, Maenhaut-Michel G, Mine N, Van Melderen L. What is the benefit to Escherichia coli of having multiple toxin-antitoxin systems in its genome? J Bacteriol. 2007;189:6101–6108. [PMC free article] [PubMed]
59. Magnuson RD. Hypothetical functions of toxin-antitoxin systems. J Bacteriol. 2007;189:6089–6092. [PMC free article] [PubMed]
60. Keren I, Kaldalu N, Spoering A, Wang Y, Lewis K. Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett. 2004;230:13–18. [PubMed]
61. Keren I, Shah D, Spoering A, Kaldalu N, Lewis K. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol. 2004;186:8172–8180. [PMC free article] [PubMed]
62. Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 2006;6:53. [PMC free article] [PubMed]
63. Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 2005;33:966–976. [PMC free article] [PubMed]
64. Gronlund H, Gerdes K. Toxin-antitoxin systems homologous with relBE of Escherichia coli plasmid P307 are ubiquitous in prokaryotes. J Mol Biol. 1999;285:1401–1415. [PubMed]
65. Mittenhuber G. Occurrence of mazEF-like antitoxin/toxin systems in bacteria. J Mol Microbiol Biotechnol. 1999;1:295–302. [PubMed]
66. Ogura T, Hiraga S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci U S A. 1983;80:4784–4788. [PMC free article] [PubMed]
67. Jensen RB, Gerdes K. Programmed cell death in bacteria: proteic plasmid stabilization systems. Mol Microbiol. 1995;17:205–210. [PubMed]
68. Gerdes K, Rasmussen PB, Molin S. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A. 1986;83:3116–3120. [PMC free article] [PubMed]
69. Lehnherr H, Maguin E, Jafri S, Yarmolinsky MB. Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J Mol Biol. 1993;233:414–428. [PubMed]
70. Wang NR, Hergenrother PJ. A continuous fluorometric assay for the assessment of MazF ribonuclease activity. Anal. Biochem. 2007;371:173–183. [PMC free article] [PubMed]
71. Arcus VL, Rainey PB, Turner SJ. The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005;13:360–365. [PubMed]
72. Llosa M, Gomis-Ruth FX, Coll M, de la Cruz Fd F. Bacterial conjugation: a two-step mechanism for DNA transport. Mol Microbiol. 2002;45:1–8. [PubMed]
73. Llosa M, de la Cruz F. Bacterial conjugation: a potential tool for genomic engineering. Res Microbiol. 2005;156:1–6. [PubMed]
74. Engelberg-Kulka H, Amitai S, Kolodkin-Gal I, Hazan R. Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet. 2006;2:e135. [PMC free article] [PubMed]
• REF 6. Moritz and Hergenrother: The Prevalence of Plasmids and Other Mobile Genetic Elements in Clinically-Important Drug-Resistant Bacteria.
This paper presents a comprehensive review of the mobile genetic elements that contribute to the dissemination of genes conferring antibiotic resistance that are associated with a number of the most problematic bacterial pathogens.
•REF 12. Fernandez-Lopez et al.: Unsaturated fatty acids are inhibitors of bacterial conjugation. This study reports the development of a fluorometric conjugation assay that detects plasmid transfer via the production and activity of luciferase. This assay was used in a high-throughput screen and identified dehydrocrepenynic acid (DHCA) and linoleic acid as inhibitors of plasmid R388 conjugation.
• REF 13. Garcillan-Barcia et al.: Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodoes.
This study utilized the recently developed technology of bacterial cytoplasmic antibody expression to create a library of intrabodies that were found to bind the TrwC relaxase domain encoded by plasmid R388. Expression of the intrabodies in the recipient cell inhibited conjugation, further confirming the transfer of a functional relaxase in conjugal DNA transfer.
•• REF 14. Lujan et al.: Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase.
This report highlights the ability of several bisphosphonates to bind the F plasmid TraI relaxase domain inhibit conjugation, and selectively kill bacteria that harbor the F plasmid and functional TraI. Two of these bisphosphonates are clinically approved, making them interesting candidates for novel antibiotic therapy.
• REF 15. DeNap et al: Combating drug-resistant bacteria: small molecule mimics of plasmid incompatibility as antiplasmid compounds.
This study combined with [16] report the binding of apramycin to the repA SLI RNA of an IncB plasmid, shutting down repA translation, inhibiting plasmid replication, and thus eliminating plasmids from the populations. In this way, apramycin act as small molecule mimic of plasmid incompatibility.
••REF 18. Mortiz and Hergenrother: Toxin-antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci.
This paper reports a comprehensive survey of the prevalence of toxin-antitoxin (TA) genes on plasmids within individual clinical isolates of VRE. Analysis of 75 isolates revealed that TA genes are ubiquitous on plasmids in VRE, and that certain individual TA systems are highly prevalent.
••REF 61. Pandey and Gerdes: Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes.
This exhaustive database search of 126 sequenced prokaryotic genomes identified 671 toxin-antitoxin (TA) loci representing the 7 major TA system families in free-living prokaryotes; whereas in contrast, obligate intracellular prokaryotes were found to lack the genes for TA systems. The observed TA systems were commonly clustered with mobile genetic elements.
PubReader format: click here to try

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links