Colicinogeny and related phenomena

Mathematical Models of Plasmid Population Dynamics

With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.

Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins

INTRODUCTION

The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized.

AREAS COVERED

We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect.

EXPERT OPINION

The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.

The Ecology and Evolution of Microbial Defense Systems in Escherichia coli

Microbes produce an extraordinary array of microbial defense systems. These include broad-spectrum classical antibiotics critical to human health concerns; metabolic by-products, such as the lactic acids produced by lactobacilli; lytic agents, such as lysozymes found in many foods; and numerous types of protein exotoxins and bacteriocins. The abundance and diversity of this biological arsenal are clear. Lactic acid production is a defining trait of lactic acid bacteria. Bacteriocins are found in almost every bacterial species examined to date, and within a species, tens or even hundreds of different kinds of bacteriocins are produced. Halobacteria universally produce their own version of bacteriocins, the halocins. Streptomycetes commonly produce broad-spectrum antibiotics. It is clear that microbes invest considerable energy in the production and elaboration of antimicrobial mechanisms. What is less clear is how such diversity arose and what roles these biological weapons play in microbial communities. One family of microbial defense systems, the bacteriocins, has served as a model for exploring evolutionary and ecological questions. In this review, current knowledge of how the extraordinary range of bacteriocin diversity arose and is maintained in one species of bacteria, Escherichia coli, is assessed and the role these toxins play in mediating microbial dynamics is discussed.

Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community

BACKGROUND

Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the colicin operon and thus influence antibiotic-mediated community dynamics.

RESULTS

Here, we investigate the community dynamics of colicin-producing, -sensitive, and -resistant/non-producer E. coli strains that colonize a microfabricated spatially-structured habitat. Nutrients are found to strongly influence community dynamics: when growing on amino acids and peptides, colicin-mediated competition is intense and the three strains do not coexist unless spatially separated at large scales (millimeters). Surprisingly, when growing on sugars, colicin-mediated competition is minimal and the three strains coexist at the micrometer scale. Carbon storage regulator A (CsrA) is found to play a key role in translating the type of nutrients into the observed community dynamics by controlling colicin release. We demonstrate that by mitigating lysis, CsrA shapes the community dynamics and determines whether the three strains coexist. Indeed, a mutant producer that is unable to suppress colicin release, causes the collapse of biodiversity in media that would otherwise support co-localized growth of the three strains.

CONCLUSIONS

Our results show how the environmental regulation of an antagonistic trait shapes community dynamics. We demonstrate that nutrient-responsive regulation of colicin release by CsrA, determines whether colicin producer, resistant non-producer, and sensitive strains coexist at small spatial scales, or whether the sensitive strain is eradicated. This study highlights how molecular-level regulatory mechanisms that govern interference competition give rise to community-level biodiversity patterns.

Pervasive domestication of defective prophages by bacteria

Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the bacterial genome. We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. The size distribution of prophage elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic degradation. Accordingly, we observed a pervasive pattern of systematic counterselection of nonsynonymous mutations in prophage genes. Importantly, such patterns of purifying selection are observed not only on accessory regions but also in core phage genes, such as those encoding structural and lysis components. This suggests that bacterial hosts select for phage-associated functions. Several of these conserved prophages have gene repertoires compatible with described functions of adaptive prophage-derived elements such as bacteriocins, killer particles, gene transfer agents, or satellite prophages. We suggest that bacteria frequently domesticate their prophages. Most such domesticated elements end up deleted from the bacterial genome because they are replaced by analogous functions carried by new prophages. This puts the bacterial genome in a state of continuous flux of acquisition and loss of phage-derived adaptive genes.

Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in enterobacterial blooms

The host's immune system plays a key role in modulating growth of pathogens and the intestinal microbiota in the gut. In particular, inflammatory bowel disorders and pathogen infections induce shifts of the resident commensal microbiota which can result in overgrowth of Enterobacteriaceae (“inflammation-inflicted blooms”). Here, we investigated competition of the human pathogenic Salmonella enterica serovar Typhimurium strain SL1344 (S. Tm) and commensal E. coli in inflammation-inflicted blooms. S. Tm produces colicin Ib (ColIb), which is a narrow-spectrum protein toxin active against related Enterobacteriaceae. Production of ColIb conferred a competitive advantage to S. Tm over sensitive E. coli strains in the inflamed gut. In contrast, an avirulent S. Tm mutant strain defective in triggering gut inflammation did not benefit from ColIb. Expression of ColIb (cib) is regulated by iron limitation and the SOS response. CirA, the cognate outer membrane receptor of ColIb on colicin-sensitive E. coli, is induced upon iron limitation. We demonstrate that growth in inflammation-induced blooms favours expression of both S. Tm ColIb and the receptor CirA, thereby fuelling ColIb dependent competition of S. Tm and commensal E. coli in the gut. In conclusion, this study uncovers a so-far unappreciated role of inflammation-inflicted blooms as an environment favouring ColIb-dependent competition of pathogenic and commensal representatives of the Enterobacteriaceae family.

Colicins are bacterial protein toxins which show potent activity against sensitive strains in vitro. Ecological models suggest that colicins play a major role in modulating dynamics of bacterial populations in the gut. However, previous studies could not readily confirm these predictions by respective in vivo experiments. In animal models, colicin-producing strains only show a minor or even absent fitness benefit over sensitive competitors. Here, we propose that the gut environment plays a crucial role in generating conditions for bacterial competition by colicin Ib (ColIb). Gut inflammation favours overgrowth of Enterobacteriaceae (“inflammation-inflicted Enterobacterial blooms”). We show that a pathogenic Salmonella Typhimurium (S. Tm) strain benefits from ColIb production in competition against commensal E. coli upon growth in inflammation-inflicted blooms. In the absence of gut inflammation, ColIb production did not confer a competitive advantage to S. Tm. In the inflamed gut, the genes for ColIb production in S. Tm and its corresponding ColIb-surface receptor CirA in E. coli were markedly induced, as compared to the non-inflamed gut. Therefore, environmental conditions in inflammation-inflicted blooms favour colicin-dependent competition of Enterobacteriaceae by triggering ColIb production and susceptibility at the same time. Our findings reveal a role of colicins as important bacterial fitness factors in inflammation-induced blooms.

Bacteriocinogeny in experimental pigs treated with indomethacin and Escherichia coli Nissle

AIM: To evaluate bacteriocinogeny in short-term high-dose indomethacin administration with or without probiotic Escherichia coli Nissle 1917 (EcN) in experimental pigs.

METHODS: Twenty-four pigs entered the study: Group A (controls), Group B (probiotics alone), Group C (indomethacin alone) and Group D (probiotics and indomethacin). EcN (3.5 × 10¹⁰ bacteria/d for 14 d) and/or indomethacin (15 mg/kg per day for 10 d) were administrated orally. Anal smears before and smears from the small and large intestine were taken from all animals. Bacteriocin production was determined with 6 different indicator strains; all strains were polymerase chain reaction tested for the presence of 29 individual bacteriocin-encoding determinants.

RESULTS: The general microbiota profile was rather uniform in all animals but there was a broad diversity in coliform bacteria (parallel genotypes A, B1, B2 and D found). In total, 637 bacterial strains were tested, mostly Escherichia coli (E. coli). There was a higher incidence of non-E. coli strains among samples taken from the jejunum and ileum compared to that of the colon and rectum indicating predominance of E. coli strains in the large intestine. Bacteriocinogeny was found in 24/77 (31%) before and in 155/560 (28%) isolated bacteria at the end of the study. Altogether, 13 individual bacteriocin types (out of 29 tested) were identified among investigated strains. Incidence of four E. coli genotypes was equally distributed in all groups of E. coli strains, with majority of genotype A (ranging from 81% to 88%). The following types of bacteriocins were most commonly revealed: colicins Ia/Ib (44%), microcin V (18%), colicin E1 (16%) and microcin H47 (6%). There was a difference in bacteriocinogeny between control group A (52/149, 35%) and groups with treatment at the end of the study: B: 31/122 (25%, P = 0.120); C: 43/155 (28%, P = 0.222); D: 29/134 (22%, P = 0.020). There was a significantly lower prevalence of colicin Ib, microcins H47 and V (probiotics group, P < 0.001), colicin E1 and microcin H47 (indomethacin group, P < 0.001) and microcins H47 and V (probiotics and indomethacin group, P = 0.025) compared to controls. Escherichia fergusonii (E. fergusonii) was identified in 6 animals (6/11 isolates from the rectum). One strain was non-colicinogenic, while all other strains of E. fergusonii solely produced colicin E1. All animals started and remained methanogenic despite the fact that EcN is a substantial hydrogen producer. There was an increase in breath methane (after the treatment) in 5/6 pigs from the indomethacin group (C).

CONCLUSION: EcN did not exert long-term liveability in the porcine intestine. All experimental pigs remained methanogenic. Indomethacin and EcN administered together might produce the worst impact on bacteriocinogeny.

Microbially-produced peptides having potential application to the prevention of dental caries

Strategies advanced to decrease the occurrence of dental caries have in the past typically focussed upon attempting to reduce plaque accumulation by application of broad-spectrum antibacterial agents. In recent years however there has been growing interest in the application of a more targeted approach to the selective elimination from plaque of those bacterial species that are specifically implicated as the aetiological agents of this disease. This review focuses upon a number of the small bacterially-produced peptide antibiotics known as bacteriocins that are currently being explored for their potential role in the treatment and prevention of dental caries.

Bacterioides fragilis: production and sensitivity to bacteriocins

Bacteriocin production and sensitivity to bacteriocins have been successfully applied as an epidemiological tool in several species of bacteria. However, little work has been carried out on the bacteriocins produced by Bacteroides fragilis, which is the most frequently isolated anaerobe species from clinical specimens. Thirty two clinical isolates of B. fragilis grown anaerobically on a 0.22 microm membrane filter spotted on an agar plate, were tested for bacteriocin production and used in a screen for bacteriocin sensitivity. Sensitivity to at least one bacteriocin was found in 94% of the strains, 62.5% were sensitive to two bacteriocins, whereas 34.4% were sensitive to three or more and finally one strain was found sensitive to 17 bacteriocins. Of the strains studied, 94% inhibited at least one strain, 66% inhibited two strains, and 30% inhibited at least three strains or more. Finally, one strain was extremely active by inhibiting the growth of 17 strains. Bacteriocin types are characterised by geographic variation, and their epidemiological investigation by a simple method could be promoted.

Sublethal concentrations of ciprofloxacin induce bacteriocin synthesis in Escherichia coli

Antibiotics that interfere with DNA replication, as well as cell wall synthesis, induce the SOS response. In this report, we show that ciprofloxacin induces synthesis of colicins, narrow-spectrum antibiotics frequently produced by Escherichia coli strains, in an SOS-dependent manner.

Measurements of fitness and competition in commensal Escherichia coli and E. coli O157:H7 strains

Although the main reservoirs for pathogenic Escherichia coli O157:H7 are cattle and the cattle environment, factors that affect its tenure in the bovine host and its survival outside humans and cattle have not been well studied. It is also not understood what physiological properties, if any, distinguish these pathogens from commensal counterparts that live as normal members of the human and bovine gastrointestinal tracts. To address these questions, individual and competitive fitness experiments, indirect antagonism assays, and antibiotic resistance and carbon utilization analyses were conducted using a strain set consisting of 122 commensal and pathogenic strains. The individual fitness experiments, under four different environments (rich medium, aerobic and anaerobic; rumen medium, anaerobic; and a minimal medium, aerobic) revealed no differences in growth rates between commensal E. coli and E. coli O157:H7 strains. Indirect antagonism assays revealed that E. coli O157:H7 strains more frequently produced inhibitory substances than commensal strains did, under the conditions tested, although both groups displayed moderate sensitivity. Only minor differences were noted in the antibiotic resistance patterns of the two groups. In contrast, several differences between commensal and O157:H7 groups were observed based on their carbon utilization profiles. Of 95 carbon sources tested, 27 were oxidized by commensal E. coli strains but not by the E. coli O157:H7 strains. Despite the observed physiological and biochemical differences between these two groups of E. coli strains, however, the O157:H7 strains did not appear to possess traits that would confer advantages in the bovine or extraintestinal environment.

Bacteriocins: evolution, ecology, and application

Microbes produce an extraordinary array of microbial defense systems. These include classical antibiotics, metabolic by-products, lytic agents, numerous types of protein exotoxins, and bacteriocins. The abundance and diversity of this potent arsenal of weapons are clear. Less clear are their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the most abundant and diverse family of microbial defense systems: the bacteriocins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics. In the latter half of this review we focus on the potential role bacteriocins may play in addressing human health concerns and the current role they serve in food preservation.

Extracellular sensing components and extracellular induction component alarmones give early warning against stress in Escherichia coli

The work reported here follows from the proposal that, for efficient induction of numerous extracellular stress responses, cultures contain extracellular stress-sensing molecules, termed extracellular sensing components (ESCs). These are directly converted to extracellular induction components (EICs) by stresses, thus providing an early warning system against stress, with very rapid responses occurring on exposure to increasing levels of stress. Although some stress responses appear to involve activation of intracellular sensors, the proposed ESCs and EICs function for many stress tolerance and sensitization responses and for several cross-tolerance and cross-sensitization responses. Because EICs can induce responses in unstressed cells, and because they are small molecules that can diffuse away from the site of formation, they can be considered to be 'alarmones', both warning unstressed organisms of future stress and preparing both stressed and unstressed ones to resist it. Therefore, EICs produced by one group of organisms could affect another group i.e. there could be 'cross-talk' (cell-to-cell communication) with other organisms in an area, to which the EICs diffuse, that has not yet faced the stress. In particular, stimuli that switch on acid tolerance, alkali tolerance, pH sensitization responses and alkylhydroperoxide tolerance are detected by ESCs; these molecules can give rise to EICs in the presence of the stress without organisms needing to be present. Not only does the ESC-EIC interconversion allow rapid switching on of responses, but for some responses it also allows rapid switching off. For some ESCs, the sensor can be modified by the culture conditions, modification leading to altered responsiveness to stress; such sensor changes appear to have evolved to allow the most efficient responses to stress to occur, under defined sets of conditions. In addition, the receptors on the organisms that interact with EICs are modified by culture conditions, so that extracellular components that function as ESCs for some cultures can act as EICs for others. In view of their role in early warning of stress, EICs and ESCs are likely to have important functions in the natural environment, especially in natural waters, in foods and food preparation and production, in hospital, domestic and commercial locations, and in the animal and human body. Findings of major importance relate to the extreme stress tolerance of some EICs. For example, because the acid-tolerance EIC formed at pH 5.0 is a heat-resistant molecule, heat-killed suspensions of acid-tolerant cultures can confer acid tolerance on living E. coli; cultures killed by extreme acidity and alkalinity and by exposure to high levels of UV irradiation or novobiocin are also able to confer acid tolerance on living E. coli. Extracellular components that inhibit induction of stress responses also occur in enterobacteria, since it has been found that AMP and HCO3-, which inhibit acid-tolerance induction, do so by forming extracellular agents that block the functioning of EICs. Similar agents to the above EICs and ESCs may occur in other non-stress-related processes. Systems using these extracellular components are quite distinct in their properties from quorum-sensing systems in Gram-negative bacteria and from those systems that use small peptides in intercellular communication and which induce virulence-related enzyme synthesis in Staphylococcus aureus and competence in streptococci and bacilli. Additionally, probably because the ESCs have evolved to become modified by cultural conditions, the components in the stress-related systems, although relatively small proteins, are much larger than the extracellular components used in the quorum-sensing processes and related systems. It is possible that the extracellular 'protectants' of Nikolaev, which protect E. coli from stress, act similarly to the EICs described here, e.g. by inducing stress tolerance. The antimutagenic factor of Vorobjeva may act similarly, although there is no evidence, so far, to suggest that it acts by inducing tolerance to mutagens.

Production of antimicrobial substances, by hospital bacteria, active against other micro-organisms

Fifty-nine clinical strains of bacteria, isolated from patients in the Regional Hospital of Talca, were studied. Seventy-four percent of these strains produced antibacterial substances, in comparison with 18% of the same bacterial species obtained from patients from a non-hospital habitat. Almost all the bacteria isolated from hospitalized patients demonstrated in vitro resistance to different antimicrobial agents. Pseudomonas aeruginosa was the most frequent species producing antibacterial substances and its products were of high potency, with a wide spectrum of antimicrobial activity. Cure of plasmid DNA, in most of the antibacterial-producer strains, resulted in the loss of their lethal activity and they also became susceptible in vitro to anti-microbials. These results indicated that such properties are encoded in extrachromosomal DNA. We believe that the knowledge of the antimicrobial activity and resistance to antimicrobials of bacteria from a hospital habitat can help explain the selection and persistence of such strains in this particular ecological niche.

Characterization of the cvaA and cvi promoters of the colicin V export system: iron-dependent transcription of cvaA is modulated by downstream sequences

Secretion of the Escherichia coli toxin colicin V was previously determined to be iron regulated via the Fur (ferric uptake regulator) protein, based on studies in fur mutants. The iron dependence of transcription and expression of cvaA, which encodes a transporter accessory protein, and cvi, encoding the colicin V immunity protein, was assessed under conditions of iron excess or depletion. Immunoblots showed that production of both Cvi and CvaA is iron dependent. The iron-dependent transcriptional start for cvaA identified by primer extension and S1 nuclease analysis, P1, lies 320 bp upstream of the translational start and is associated with a newly identified Fur binding site. Beta-galactosidase activity in transcriptional lacZ fusions with the P1 promoter alone is higher than with downstream sequences present and is induced 10-fold by iron depletion. Including immediate downstream regions with P1 enhances activity from P1 even more but reduces the induction by iron depletion fivefold. Including subsequent downstream sequences, however, down-modulates overall transcription from P1 almost fourfold. Deletion of a long stem-loop structure in this region alleviates the down-modulation by increasing transcription, indicating that the sequences or structure of this element may contribute to this down-regulation. Characterization of the cvi promoter by primer extension showed that it resides where predicted, about 50 bp upstream of cvi associated with a previously identified Fur binding site. The cvi promoter is also inducible by iron depletion. The modulating sequences from cvaA were placed downstream of the cvi promoter to test their effects in transcriptional fusions of the cvi promoter to lacZ. The fusion results showed that these sequences also modulate transcription of the cvi promoter in a manner similar to that of the cvaA promoter. The potential for up- and down-regulation within the long untranslated region downstream of the cvaA promoter suggests a novel mechanism that fine-tunes expression of the colicin V secretion genes.

Structure and function of plasmid pColD157 of enterohemorrhagic Escherichia coli O157 and its distribution among strains from patients with diarrhea and hemolytic-uremic syndrome

In this study, pColD157, a 6.7-kb colicinogenic plasmid of enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain CL40cu, was characterized by restriction mapping and determination of its complete nucleotide sequence. The sequence consists of 6,675 bp and shows a high degree of similarity to the nucleotide sequence of colicinogenic plasmids pColD-CA23 and pColK. Seven potential genes were located on pColD157, three of which were closely related (>97.9%) to the colicin D structural gene and the corresponding immunity and lysis genes of plasmid pColD-CA23, and these were therefore designated cda, cdi, and cdl, respectively, using the reference extension -CL40 for differentiation. The adjacent 3' region is related to the origin of replication of pColD-CA23. In contrast, the remaining part of the plasmid harbors a cluster of genes, closely related to the mobilization genes of pColK, which is followed by a 0.3-kb stretch homologous to the pColK resolution function. These determinants were designated mbdA, mbdB, mbdC, and mbdD and cdr, respectively. Southern blot analysis was performed with a probe specific for the cda gene of pColD157 and two groups of EHEC O157:H7 isolates from patients with diarrhea or hemolytic-uremic syndrome resident in Germany. Whereas 16 of 46 E. coli O157 strains isolated between 1987 and 1991 harbored plasmid pColD157, only 1 of 50 strains isolated during 1996 carried this plasmid. In addition, all strains harboring plasmid pColD157 were shown to have colicinogenic activity.

Interactions of dedicated export membrane proteins of the colicin V secretion system: CvaA, a member of the membrane fusion protein family, interacts with CvaB and TolC

The antibacterial peptide toxin colicin V uses a dedicated signal sequence-independent system for its secretion in Escherichia coli and requires the products of three genes, cvaA, cvaB, and tolC. As a member of the membrane fusion protein family, CvaA is supposed to form a bridge that connects the inner and outer membranes via interaction with CvaB and TolC, respectively. In this study, we investigated the possible interaction of these proteins. When CvaA or CvaB was absent, the corresponding amount of CvaB or CvaA, respectively, was decreased, and the amounts of both proteins were reduced when TolC was depleted. Translational lacZ fusions showed that TolC did not affect the synthesis of either CvaA-beta-galactosidase or CvaB-beta-galactosidase, and CvaA or CvaB did not affect the synthesis of CvaB-beta-galactosidase or CvaA-beta-galactosidase, respectively. However, the stabilities of CvaA and CvaB proteins were affected by the absence of one another and by that of TolC. The instability of CvaA was more severe in TolC-depleted cells than in CvaB-depleted cells. On the other hand, CvaB was less stable in the absence of CvaA than in the absence of TolC. In addition, using a cross-linking reagent, we showed that CvaA directly interacts with both CvaB and TolC proteins. Taken together, these data support the hypothesized structural role of CvaA in connecting CvaB and TolC.

Yeast killer systems

The killer phenomenon in yeasts has been revealed to be a multicentric model for molecular biologists, virologists, phytopathologists, epidemiologists, industrial and medical microbiologists, mycologists, and pharmacologists. The surprisingly widespread occurrence of the killer phenomenon among taxonomically unrelated microorganisms, including prokaryotic and eukaryotic pathogens, has engendered a new interest in its biological significance as well as its theoretical and practical applications. The search for therapeutic opportunities by using yeast killer systems has conceptually opened new avenues for the prevention and control of life-threatening fungal diseases through the idiotypic network that is apparently exploited by the immune system in the course of natural infections. In this review, the biology, ecology, epidemiology, therapeutics, serology, and idiotypy of yeast killer systems are discussed.

Characterization of in-frame proteins encoded by cvaA, an essential gene in the colicin V secretion system: CvaA* stabilizes CvaA to enhance secretion

Colicin V (ColV), an antibacterial peptide toxin, uses a dedicated signal sequence-independent export system for its extracellular secretion in Escherichia coli. The products of at least three genes (a chromosomal tolC gene and two plasmid-born cvaA and cvaB genes) are involved in this process. To characterize the gene products, the cvaA gene was subcloned and expressed under the control of T7 RNA polymerase promoter. Two in-frame proteins, CvaA and CvaA*, were expressed and identified. DNA sequences predicted that both proteins have two potential translational initiation sites. N-terminal peptide sequencing showed that the translation of CvaA starts from a TTG, 11 amino acids upstream of the previously proposed ATG initiation site. CvaA* is translated from an upstream ATG. Expression of both CvaA and CvaA* was induced by the iron chelator 2,2'-dipyridyl, indicating that cvaA is negatively regulated at least partially by Fur. CvaA*-depleted cells were found to secrete less ColV, based on reduced activity in the supernatant, than did wild type, which was recovered by the addition of a plasmid producing CvaA*. Interestingly, CvaA*-depleted and wild-type cells had similar levels of intracellular ColV activity. Translational fusions showed that the syntheses of ColV and CvaA are not affected by CvaA* depletion. However, CvaA in CvaA*-depleted cells was less stable than that in wild-type cells, indicating that CvaA* may directly or indirectly affect the stability of CvaA. We conclude that CvaA* is not essential for ColV secretion but that it enhances the ColV secretion by stabilizing the CvaA protein.

Bacteriocins: nature, function and structure

Bacteriocins are extracellular substances produced by different types of bacteria, including both Gram positive and Gram negative species. They can be produced spontaneously or induced by certain chemicals such as mitomycin C. They are biologically one of the important substances, and have been found to be useful in membrane studies and also in typing pathogenic microorganisms causing serious nosocomial infections. Bacteriocins are a heterogeneous group of particles with different morphological and biochemical entities. They range from a simple protein to a high molecular weight complex: the active moiety of each molecule in all cases seems to be protein in nature. The genetic determinants of most of the bacteriocins are located on the plasmids, apart from few which are chromosomally encoded. These bactericidal particles are species specific. They exert their lethal activity through adsorption to specific receptors located on the external surface of sensitive bacteria, followed by metabolic, biological and morphological changes resulting in the killing of such bacteria. This review summarises the classification, biochemical nature, morphology and mode of action of bacteriocins as well as their genetic determinants and the microbiological relevance of these bactericidal agents.

Lateral transfer of rfb genes: a mobilizable ColE1-type plasmid carries the rfbO:54 (O:54 antigen biosynthesis) gene cluster from Salmonella enterica serovar Borreze

Plasmid pWQ799 is a 6.9-kb plasmid isolated from Salmonella enterica serovar Borreze. Our previous studies have shown that the plasmid contains a functional biosynthetic gene cluster for the expression of the O:54 lipopolysaccharide O-antigen of this serovar. The minimal replicon functions of pWQ799 have been defined, and a comparison with nucleotide and protein databases revealed this replicon to be virtually identical to ColE1. This is the first report of involvement of ColE1-related plasmids in O-antigen expression. The replicon of pWQ799 is predicted to encode two RNA molecules, typical of other ColE1-type plasmids. RNAII, the putative replication primer from pWQ799, shares regions of homology with RNAII from ColE1. RNA1 is an antisense regulator of DNA replication in ColE1-related plasmids. The coding region for RNAI from pWQ799 shares no homology with any other known RNAI sequence but is predicted to adopt a secondary structure characteristic of RNAI molecules. pWQ799 may therefore represent a new incompatibility group within this family. pWQ799 also possesses cer, rom, and mob determinants, and these differ minimally from those of ColE1. The plasmid is mobilizable in the presence of either the broad-host-range helper plasmid pRK2013 or the IncI1 plasmid R64drd86. Mobilization and transfer of pWQ799 to other organisms provides the first defined mechanism for lateral transfer of O-antigen biosynthesis genes in S. enterica and explains both the distribution of related plasmids and coexpression of the O:54 factor with other O-factors in different Salmonella serovars. The base composition of the pWQ799 replicon sequences gives an average percent G+C value typical of Salmonella spp. In contrast, the percent G+C value is dramatically lower with rfb0:54, consistent with the possibility that the cluster was acquired from an organism with much lower G+C composition.

Colicins: structures, modes of action, transfer through membranes, and evolution

This article intends to inform a broader audience on a fascinating class of protein toxins (bacteriocins) which usually kill only cells of the same species. Those who gained a deeper interest in bacteriocins can find a comprehensive description of the field in a recent book based on a conference (James et al. 1992), and in more specialized review articles dealing with certain aspects (Pugsley 1984a, b), or certain colicins (De Graaf and Oudega 1986; Harkness and Olschläger 1991; Lazdunski et al. 1988). The older literature has been reviewed by Brandis and Smarda (1971), Reeves (1972), Hardy (1975) and Konisky (1982).

A novel transposon-like structure carries the genes for pyocin AP41, a Pseudomonas aeruginosa bacteriocin with a DNase domain homology to E2 group colicins

The genetic determinant for pyocin AP41, a bacteriocin produced by Pseudomonas aeruginosa, has been cloned. The determinant is located on the chromosome flanked by a pair of inverted repeats, forming a transposon-like structure (TnAP41). TnAP41 possesses some features characteristic of the Tn3 family of transposons. Based on a comparison with the structure of the corresponding region of the chromosome of a non-producer strain, we propose that P. aeruginosa has acquired pyocinogeny by the transposition of TnAP41 into the chromosome. The determinant comprises two ORFs encoding the protein subunits responsible for the killing action (the large component) and immunity (the small component). Amino acid sequences of the C-terminus of the large component (the deoxyribonuclease domain) and the immunity protein show remarkable homology to those of E2 group colicins, suggesting that these bacteriocins, which are produced by distantly related species, have originated from a common ancestor.

Colicin V virulence plasmids

ColV plasmids are a heterogeneous group of IncFI plasmids which encode virulence-related properties such as the aerobactin iron uptake system, increased serum survival, and resistance to phagocytosis. These plasmids have been found in invasive strains of Escherichia coli which infect vertebrate hosts including humans and livestock. Colicin V was the first colicin to be identified, in 1925, but not until the field experienced a renewed interest has the mechanism of colicin V activity been explored. As encoded by ColV plasmid pColV-K30, the aerobactin iron uptake system has been extensively investigated, but other ColV-encoded phenotypes remain largely uncharacterized. Restriction enzyme mapping of the 144-kb pColV-K30 and of the 80-kb pColV-B188 has facilitated systematic study, so that questions can be addressed by a molecular and comparative approach regarding the contributions of individual factors and plasmids to the virulence of host E. coli in model systems. The family of large ColV plasmids could be analogous to other families of large virulence plasmids, and insights gained from studying these plasmids should contribute to our understanding of cross-genetic interactions and the role of large plasmids in bacterial pathogenesis.

Organization and nucleotide sequences of two lactococcal bacteriocin operons

Two distinct regions of the Lactococcus lactis subsp. cremoris 9B4 plasmid p9B4-6, each of which specified bacteriocin production as well as immunity, have been sequenced and analyzed by deletion and frameshift mutation analyses. On a 1.8-kb ScaI-ClaI fragment specifying low antagonistic activity, three open reading frames (ORFs) were present, which were organized in an operon. The first two ORFs, containing 69 and 77 codons, respectively, were involved in bacteriocin activity, whereas the third ORF, containing 154 codons, was essential for immunity. Primer extension analysis indicated the presence of a promoter upstream of the ORFs. Two ORFs were present on a 1.3-kb ScaI-HindII fragment specifying high antagonistic activity. The first ORF, containing 75 codons, specified bacteriocin activity. The second ORF, containing 98 codons, specified immunity. The nucleotide sequences of both fragments upstream of the first ORFs as well as the first 20 bp of the first ORF of both bacteriocin operons appeared to be identical.

Haemocin, the bacteriocin produced by Haemophilus influenzae: species distribution and role in colonization

Four hundred thirty-eight strains of Haemophilus influenzae were examined for production of and sensitivity to haemocin, a bacteriocin produced by some members of this species. Whereas 199 of 212 (94%) type b isolates produced haemocin, 131 of 134 (98%) nontypeable and 91 of 92 (99%) encapsulated non-type b isolates were sensitive to haemocin. Among strains previously genetically characterized by multilocus enzyme electrophoresis, haemocin production was detected in type b isolates belonging to 25 of 29 (86%) clonally distinct electrophoretic types. None of 60 clonally distinct nontypeable strains produced this substance, and all were sensitive to it in vitro. The genes encoding haemocin production were transformed independently of the genes necessary for capsule expression from a prototypic type b strain to a nontypeable strain. After intranasal inoculation of infant rats with an equal mixture of a non-haemocin-producing strain and its haemocin-producing transformant, organisms capable of haemocin production predominated in both nasopharyngeal and blood cultures. These data demonstrate that haemocin production is strongly associated with type b encapsulated members of this species and suggest a mechanism by which haemocin might play a role in host nasopharyngeal colonization by this pathogen.

Genetic stability of the antagonistic character of Enterococcus faecalis ssp. liquefaciens and the detection of a new inhibitory bacteriocin-like substance

The inhibitory capacity of strain S-48 of Enterococcus faecalis ssp. liquefaciens was studied. The strain produces a broad-spectrum peptide antibiotic (AS-48) that has been characterized elsewhere. The isolation of mutants from S-48 after mutagenic treatment revealed another inhibitory substance which remained masked in the wild strain. The protein nature and restricted spectrum of this substance points to its being a bacteriocin.

Plasmid profiles and klebocin types in epidemiologic studies of infections by Klebsiella pneumoniae

The epidemiological methods of klebocin typing, antibiogram and plasmid DNA profile were evaluated using organisms isolated from a suspected epidemic of gentamicin-resistant Klebsiella pneumoniae and unrelated strains from different geographical areas as controls. The electrophoretic analysis of plasmid DNAs from Klebsiella pneumoniae showed the presence of at least one and up to as many as seven plasmids in each strain. The molecular weight of plasmid DNAs ranged from 1 to greater than 70 mega daltons. While none of the control Klebsiella pneumoniae strains showed identical plasmid profiles, 63% of the epidemic-related Klebsiella pneumoniae strains did. Klebocin typing and plasmid DNA profile gave different results for the same strains. Plasmid DNA profile was found to be a more valuable method than klebocin typing alone or klebocin typing in combination with antibiogram for differentiating epidemiologically related from unrelated isolates. Both plasmid DNA profile and klebocin typing methods were superior to antibiogram.

Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen

Cloned fragments of genomic DNA from the ruminal anaerobe Bacteroides ruminicola subsp. brevis B14 were isolated and used as hybridization probes to identify closely related bacterial species. One DNA fragment unique to strain B14 was tested to determine its sensitivity in detecting homologous sequences among total ruminal microbial DNA. In a DNA titration experiment, the probe was capable of detecting strain B14 sequences in vitro down to 0.1% of the total bacterial DNA present in a hybridization assay. There was no detectable signal for total ruminal bacterial DNA. The specificity of this DNA fragment was exploited to enumerate strain B14 in a fresh mixed suspension of ruminal bacteria in vitro and after inoculation of the strain into the rumen. In vitro strain B14 had a half-life of 9 h. However, following inoculation into the rumen there was a very rapid loss of the strain to below the detectable limit within 3 h. The half-life was less than 30 min. This loss was not due to ruminal dilution or to bacteriophage attack but was possibly the result of a specific bacteriocinlike activity present in the rumen and detectable in fresh ruminal fluid.

Combined use of phage typing, enterococcinotyping and species differentiation of group D streptococci as an effective epidemiological tool

Ninety-five group D streptococcal isolates from the feces of 95 healthy persons were compared with 157 group D streptococcal isolates from 38 patients of the surgical intensive care unit (sICU). The typing systems consisted of phage typing, enterococcinotyping and species differentiation. Strains isolated from fecal specimens showed high individuality (66 combination types) whereas strains from the sICU revealed strongly uniform types (32 combination types, three types comprised 83 isolates, i.e. 52.8%). Endogenous colonization was demonstrated by isolation of strains from different locations (throat, trachea, wounds, blood, urine, drains, catheters, and vaginal swabs) from the same patient, and routes of transmission of the same strains to several patients were traced. The combination of three systems revealed a good discrimination between isolates of fecal and extrafecal specimens. The investigation detected highly preferred types in strains of extrafecal origin which were rarely isolated from fecal specimens. This may indicate that only strains with special characters preferably were able to colonize extraintestinal sites.

Four plasmid genes are required for colicin V synthesis, export, and immunity

The colicin V production and immunity genes were isolated from plasmid pColV-K30. A HindIII-to-SalI fragment of 9.4 kilobases was cloned into the compatible vectors pBR322 and pACYC184. Mutants defective in colicin production were generated by Tn5 insertions and by constructing deletions in vitro. Physical analysis of these mutations identified a 4.4-kilobase region of this DNA which contains all the plasmid genes (cva) needed for the production of colicin V. The colicin V immunity determinant (cvi) is in a 700-base-pair fragment located within one end of this region. Complementation tests identified three genes, called cvaA, cvaB, and cvaC, required for colicin production. Analysis of the proteins labeled in minicells harboring various Tn5 insertions allowed us to identify protein products for the cvaA and cvaC genes. Mutations in cvaA and cvaB eliminated colicin activity in culture supernatants, but not within the cells. Mutations in cvaC, however, eliminated all detectable activity. From these results we conclude that the cvaC gene codes for the structural gene for colicin V, while cvaA and cvaB are apparently needed for the normal export of the colicin.

Purification and biochemical properties of a bacteriocin from Actinobacillus actinomycetemcomitans

Extracts of certain strains of Actinobacillus actinomycetemcomitans are inhibitory to strains of Streptococcus sanguis such as S. sanguis ATCC 10556. The isolation of a protein from an A. actinomycetemcomitans sonic extract which copurified with the inhibitory activity was accomplished by preparative isoelectric focusing, Sephadex G-100 gel filtration chromatography, and preparative polyacrylamide gel electrophoresis (PAGE). The resulting isolated protein, which focused at a pH of 6.1 to 6.3, appeared as a single band in anionic nondissociating PAGE analysis. This protein could be dissociated into two subunits with molecular weights of 50,000 and 70,000, which were resolvable by PAGE analysis. A 1,758-fold increase in specific activity was seen in the purified inhibitory protein compared with the crude sonic extract starting material. The properties of the inhibitory activity in the A. actinomycetemcomitans extract are characteristic of a bacteriocin. Accordingly, we propose the name actinobacillicin for the inhibitory protein.

Recognition of T-cell murine leukemia by bacteriocin (colicin); correlation with transplantation experiments

The presence of potential murine leukemia and overt leukemia cells in various organs at different phases of leukemogenesis was demonstrated by transplantation experiments and sensitivity to bacteriocin (colicin HSC10). Such correlation was found in three experimental models: AKR mice developing spontaneous T-cell leukemia and BL/6 mice infected with radiation leukemia virus variants inducing a high or low overt T-cell leukemia incidence. The sensitivity to bacteriocin was evaluated by testing the cell cycle perturbation following in-vitro incubation of lymphoid cells with colicin (or Tris buffer as controls) monitored by flow-cytometry. The analysis was based on measuring relative differences in fluorescence intensity of propidium iodide stained DNA in the individual cells. The interaction with colicin of leukemic cells and lymphoid cells containing potential leukemic cells (PLC) resulted in a reduction in the cell number of the G0/G1 and SG2M phases while cells accumulated in the "pre-G1" channels. In contrast, normal lymphoid cells exposed to bacteriocin did not show such changes in the DNA histograms. The distribution pattern of PLC in the thymus and spleen (in the models tested) obtained by transplantation studies coincided with sensitivity of spleen and thymus cells to colicin. However, in most instances, the PLC in the bone marrow were not recognized by colicin, but their leukemogenic potential was reduced following interaction with colicin as shown by PLC transplantation studies. It is thus suggested that colicin might be used for identification and eradication of transformed cells.

Bacteriocinlike Activity within the Genus Thermus

Members of the genus Thermus were examined for the presence of bacteriocinlike inhibitory activity. Testing was done by the deferred antagonism technique. Antagonistic activity, as evidenced by zones of inhibition, was expressed by Thermus rubens against all other Thermus strains tested. T. rubens itself was immune to this activity. Plasmid analysis of T. rubens revealed the presence of one plasmid of approximately 64 megadaltons.

A motility lesion in ColV+ Escherichia coli strains and its possible clinical significance

The introduction of the ColV-K30 or ColV,I-K94 plasmid into Escherichia coli strains produced derivatives which had a motility lesion if grown without shaking at 37 degrees C. Although most ColV+ organisms from shaken cultures were motile, 80-90% of free unclumped organisms from static cultures were flagellate but non-motile. This plasmid effect was temperature-dependent with only those ColV+ organisms grown at 37 degrees C being affected; ColV+ organisms grown at 30 degrees C or below were predominantly motile. The motility lesion depended on the presence, in the ColV+ organisms, of transfer and colicin components together but not of the VmpA protein. Aside from the changed motility, there was extensive autoagglutination (clumping) of ColV+ organisms in static cultures, and the two phenomena (clumping and motility lesion) appeared to be governed by the same factors. The Flac plasmid of FI incompatibility group had a slight inhibitory effect on motility of strain 1829 and caused slight clumping, but representative plasmids of groups FII, FIII, FIV, C, H, I, K, M, N, P, W and X had no appreciable effect on either parameter. Non-motile ColV+ organisms regained motility on incubation with buffered detergent solutions, suggesting that an envelope change might be responsible for the altered motility. It can be hypothesized that ColV+ organisms in the intestine would be motile and hence able to reach the intestinal epithelium for invasion but that, once such organisms had reached the tissues and bloodstream, they would be predominantly non-motile and hence might be less susceptible to phagocytosis.

Bacteriocin-resistant mutants of Erwinia chrysanthemi: possible involvement of iron acquisition in phytopathogenicity

A series of bacteriocin-resistant mutants of Erwinia chrysanthemi 3937JRH were unable to elicit soft-rot symptoms on saintpaulia plants. The loss of pathogenicity was correlated with the disappearance of one to three outer membrane polypeptides (molecular weights, about 80,000 to 90,000) whose production in wild-type strains was greatly enhanced under iron-limited growth conditions. The mutants did not exhibit altered extracellular pectinolytic or cellulolytic activities.

Effects of the virulence plasmid ColV, I-K94 on the sensitivity of Escherichia coli to putative environmental inhibitory agents

Derivatives of Escherichia coli carrying the virulence plasmid, ColV, I-K94 were more resistant than the ColV- parents to phage Mel but were more sensitive to the hydrophobic inhibitors deoxycholate, erythromycin and lysozyme. The basis for these changes in sensitivity has been examined in ColV+ mutants with altered colicin or VmpA protein levels and in ColV+ strains with repressed transfer properties.

Envelope protein changes, autoagglutination, sensitivity to hydrophobic agents and a conditional division lesion in Escherichia coli strains carrying ColV virulence plasmids

The presence of the virulence plasmids ColV,I-K94 or ColV-K30 in Escherichia coli produces a number of cell membrane and envelope changes. The most striking of these are (1) the presence of the 33K VmpA outer membrane protein and (2) the ColV-associated occurrence of autoagglutination. The VmpA protein is a plasmid-encoded outer membrane protein which is synthesized from a larger precursor. It is distinct from the chromosomally-encoded OmpA protein but resembles it in a few respects. The VmpA protein does not appear to be involved in colicin synthesis or immunity, or in plasmid transfer. This protein was found in 6 out of 8 new ColV+ isolates, but not in 2 ColIa+ strains. ColV-induced autoagglutination occurred for strains grown in static culture at 37 but not at 25 degrees C. Detergents prevented agglutination, as did the presence in a ColV+ strain of a fi+ plasmid, ColB. Autoagglutination may be a virulence phenotype. Associated with the ability of ColV+ bacteria to agglutinate was inhibition of motility. ColV+ bacteria also showed changes in envelope permeability indicated by inhibitor sensitivity and by a ColV-associated suppression of the lac Y lesion. Some ColV,I-K94+ strains showed a mucoid colonial phenotype and this ability to form mucoid colonies was efficiently transferred with ColV but apparently not without it. The mucoid ColV+ strains resembled lon mutants in UV-sensitivity, division behaviour and sensitivity to lambda phage.

Analysis of a cloned colicin Ib gene: complete nucleotide sequence and implications for regulation of expression

The complete nucleotide sequence of a 2,971 base pair EcoRI fragment carrying the structural gene for colicin Ib has been determined. The length of the gene is 1,881 nucleotides which is predicted to produce a protein of 626 amino acids and of molecular weight 71,364. The structural gene is flanked by likely promoter and terminator signals and in between the promoter and the ribosome binding site is an inverted repeat sequence which resembles other sequences known to bind the LexA protein. Further analysis of the 5' flanking sequences revealed a second region which may act either as a second LexA binding site and/or in the binding of cyclic AMP receptor protein. Comparison of the predicted amino acid sequence of colicin Ib with that of colicins A and E1 reveals localised homology. The implications of these similarities in the proteins and of regulation of the colicin Ib structural gene are discussed.

Identification of multiple-resistance (R) and colicinogeny (Col) plasmids in an epidemic Salmonella agona serotype in Rio de Janeiro

A Salmonella agona strain has caused a hospital outbreak of gastroenteritis in a pediatric unit in Rio de Janeiro. It bears two plasmids, a small (6.5 MDa molecular weight) plasmid coding for type B colicin production and a larger one (36 MDa molecular weight) determining resistance to ampicillin, gentamicin, kanamycin and trimethoprim-sulphamethoxazole. The R-plasmid, but not the Col-plasmid, is self-transferable to a Escherichia coli recipient strain. Curing for the R-plasmid was achieved by treatment with 0.05% SDS followed by incubation at 44 degrees C. It has not been possible to cure the S. agona strain for its Col-plasmid.

Genetic determinant of pyocin AP41 as an insert in the Pseudomonas aeruginosa chromosome

The genetic determinant for pyocin AP41 , a bacteriocin produced by Pseudomonas aeruginosa PAF, was transferred to P. aeruginosa PAO and analyzed. By conjugation experiments, the pyocin determinant was found to be located on the chromosome, being closely linked to argG at about 45 min on the genetic map. Cloning of the pyocin AP41 gene into the plasmid R68.45 was attempted in vivo by taking advantage of its linkage at argG. R' argG+ plasmids were isolated by interspecific conjugation between P. aeruginosa and Escherichia coli recA argG strains. Some of the R' argG+ plasmids did contain the pyocin AP41 determinant. Genetic and physical analyses of these R' plasmids indicated that the pyocin AP41 determinant was located within a 2.9-kilobase extra segment found at a certain position of the chromosome of various pyocin AP41 producer strains.

Conjugal transfer and characterization of bacteriocin plasmids in group N (lactic acid) streptococci

Thirteen bacteriocin-producing strains of group N (lactic acid) streptococci were screened for their potential to transfer this property by conjugation to Streptococcus lactis subsp. diacetylactis Bu2-60. Bacteriocin production in three strains was plasmid encoded as shown by conjugal transfer and by analysis of cured, bacteriocin-negative derivatives of the donor strains and the transconjugants. With Streptococcus cremoris strains 9B4 and 4G6 and S. lactis subsp. diacetylactis 6F7 as donors, bacteriocin-producing transconjugants were isolated with frequencies ranging from ca. 2 X 10(-2) to 2 X 10(-1) per recipient cell. Bacteriocin-producing transconjugants had acquired a 39.6-megadalton plasmid from the donor strains 9B4 and 4G6, and a 75-megadalton plasmid from the donor strain 6F7. As shown by restriction endonuclease analysis, the plasmids from strains 9B4 and 4G6 were almost identical. The plasmid from strain 6F7 yielded some additional fragments not present in the two other plasmids. In hybridization experiments any of the three plasmids strongly hybridized with each other and with some other bacteriocin but nontransmissible plasmids from other S. cremoris strains. Homology was also detected to a variety of cryptic plasmids in lactic acid streptococci.