Coexistence of incompatible plasmids in a bacterial population living under a feast and famine regime

A model is formulated to examine the possibility of (co)existence of plasmids of the same incompatibility and surface exclusion group in a bacterial population living under a feast-and-famine regime. The condition is given under which a growth rate decreasing plasmid can invade a bacterial population. It appears that in case only one plasmid type is present, the frequency of plasmid bearers will tend to a stable equilibrium if the food supply at each growth site gets exhausted and if both plasmid-free and plasmid-bearing bacteria need an equal quantity of food per cell division. If these two conditions are not satisfied, the frequency of plasmid-bearers might oscillate. Two plasmids will sometimes be able to coexist, but only if they follow different survival strategies; one with a high conjugational transfer rate and a lower fitness of its host, and the other with a low transfer rate and a higher host fitness. Coexistence of three plasmids of the same surface exclusion group is impossible.     

Sex pheromone plasmid pAD1-encoded surface exclusion protein of Enterococcus faecalis.

Summary During conjugative transfer of sex pheromone plasmids ofEnterococcus faecalis a so-called surface exclusion protein reduces the frequency with which these plasmids are transferred to cells already possessing the same plasmid. We report here the DNA sequence of a 3 .8 kb fragment of the sex pheromone plasmid pAD1 containing the structural genesea1 for surface exclusion protein and a small open reading frame (ORF) upstream ofsea1. Surface exclusion protein Seal was found to be highly homologous to the surface exclusion protein Sec10 encoded by the sex pheromone plasmid pCF10. Hybridization studies with DNA probes derived from the structural gene seal demonstrated that, with the exception of pAM373, all known sex pheromone plasmids carry a homologous gene. These studies also indicated that the genetic organization is similar in these plasmids, with the structural gene for surface exclusion protein being located 5 to that for aggregation substance.     

Surface exclusion specificity of the TraT lipoprotein is determined by single alterations in a five-amino-acid region of the protein

The TraT protein is a highly cell-surface-exposed lipoprotein specified by F-like plasmids that confers serum resistance and blocks the conjugative transfer of plasmids to cells bearing identical or closely related plasmids, a process known as surface exclusion. The TraT protein specified by the antibiotic-resistance plasmid R6-5 was purified to apparent homogeneity. When added to mating mixtures, TraT blocked the transfer of plasmids belonging to Surface Exclusion Group IV (Sfx IV) but had no significant effect on the transfer of plasmids belonging to other groups. Additionally, the purified protein has a protective effect on bacterial cells incubated in serum, indicating that it does not have to be located on the cell surface to mediate serum resistance. To localize regions of the protein that were responsible for surface exclusion specificity, the amino acid sequence of the TraT protein specified by CoIB2-K98 (Sfx II) was determined by cloning and sequencing of the corresponding gene. Comparison of the derived sequence with those of the F and R100-1 proteins indicated that surface exclusion specificity of TraT is determined by single alterations in a five-amino-acid region (residues 116-120). This was confirmed by segment swapping experiments in which the specificity of the R6-5 TraT protein (Sfx IV) was switched to that of the CoIB2-K98 protein (Sfx II). Our results suggest that the region defined by residues 116-120 is located on the external face of the outer membrane and interacts specifically with the donor cell in surface exclusion.     

Incompatibility and surface exclusion properties of H1 and H2 plasmids.

Plasmids of the H incompatibility group showed two types of surface exclusion and incompatibility interactions. Strong incompatibility and surface exclusion were evident between plasmids within the same subgroup, and recombination frequently occurred between these plasmids after antibiotic selection for the presence of two plasmids in the same cell. Weaker interactions were seen between plasmids of the different subgroups, H1 and H2, and recombination was not detected. Incompatibility between H1 and H2 plasmids led preferentially to the loss of the H1 plasmid, irrespective of the order of entry of the plasmids. These data are consistent with the hypothesis that incompatibility is negatively controlled.     

Characterization and restriction analysis of the P sex factor and the cryptic plasmid of Vibrio cholerae strain V58

The P plasmid of Vibrio cholerae is a derepressed sex factor restricted to V. cholerae and has been shown to express surface exclusion. We have isolated the plasmids of strain V58 and have found that in addition to P, two further cryptic plasmids are also present. P has a size of 68 kb as determined by both electron microscopy and restriction endonuclease analysis. These other plasmids are 34 and 4.7 kb in size. Restriction maps of P and the larger cryptic plasmid have been determined. It has been demonstrated that P differs from the standard Inc group test plasmids and also expresses a surface exclusion system. The ability of the type Inc plasmids to be transferred to V. cholerae by either liquid or filter matings and the stability of these plasmids in V. cholerae have also been examined.     

Why is entry exclusion an essential feature of conjugative plasmids?

Entry exclusion is a property of plasmids by which the cells that contain them become bad recipients in additional conjugation rounds. This work reviews entry exclusion essential features and analyzes the mechanisms of action of the best studied systems. We searched for homologs of the proteins responsible for experimentally known exclusion systems. Results were used to classify exclusion systems in families of related elements. We arrive to the conclusion that all conjugative plasmids contain at least one entry exclusion gene. Although entry exclusion genes seem to be part of the plasmid conjugative machinery, they are systematically absent in phylogenetically related type IV protein exporting machines involved in virulence for plants and animals. We infer from this fact that entry exclusion is an essential feature of conjugative plasmid biology. Mathematical models suggest that plasmids expressing entry exclusion selectively eliminate plasmids lacking it, reinforcing its essential character and suggesting that entry exclusion plays a direct role in plasmid survival. Other experimental results confirm that entry exclusion is essential for the stability of a conjugative plasmid. We suggest that entry exclusion limits the damage of lethal zygosis (bacterial death produced by excessive rounds of conjugation). Additionally, it avoids competition in a host among identical plasmid backbones. Conversely, the lack of entry exclusion in conjugative transposons can be understood as a means of generating rapid evolutionary change.     

pHH502, a plasmid with IncP and IncI alpha characters, loses the latter by a specific recA-independent deletion event

Plasmid pHH502, of molecular weight 70 X 10(6), determined resistance to tetracycline, chloramphenicol, trimethoprim, sulphonamides and mercuric chloride and was incompatible with members of IncP and IncI alpha. It resembled other plasmids of IncI alpha in the following properties: it determined pili that were morphologically and serologically I alpha pili, whose production was repressed in established plasmid-carrying (R+) cultures; its transfer was equally efficient in liquid or on solid medium; it exerted surface exclusion against other IncI alpha plasmids; it was non-transferable to Proteus. In a reproducible, recA-independent event, pHH502 gave rise to pHH502-1, a plasmid of molecular weight 40 X 10(6), lacking determinants for resistance to tetracycline and chloramphenicol and all detectable IncI alpha characteristics. pHH502-1 was incompatible only with IncP plasmids and resembled other IncP plasmids in determining constitutive production of rigid pili, in its surface exclusion, in transferring at greater frequency on solid than in liquid medium and in being transmissible to Proteus mirabilis. It differed from other IncP plasmids in the morphology and serological type of its pili and in failing to transfer to Pseudomonas aeruginosa or Acinetobacter calcoaceticus. Small numbers of pHH502-1 rigid pili were present on bacteria carrying pHH502. Possible mechanisms for the generation of pHH502 and pHH502-1 are discussed.     

Nucleotide sequence of the surface exclusion genes traS and traT from the IncF0 lac plasmid pED208.

pED208 is a 90-kilobase conjugative plasmid belonging to the incompatibility group IncF0 lac. The surface exclusion system from this plasmid was cloned and sequenced, and two genes demonstrated exclusion ability. traS encoded a 186-amino-acid hydrophobic protein which, when transcribed from a vector promoter, caused exclusion of pED208. The product of traT (TraTp) was a 245-residue protein which was highly expressed independently of a vector promoter in Escherichia coli minicells. The TraTp from pED208 was homologous with traT products from the IncF plasmids R-100 and F (80% homology), but recombinants containing the pED208 surface exclusion system excluded F poorly.     

Comparison of Proteins Involved in Pilus Synthesis and Mating Pair Stabilization from the Related Plasmids F and R100-1: Insights into the Mechanism of Conjugation

F and R100-1 are closely related, derepressed, conjugative plasmids from the IncFI and IncFII incompatibility groups, respectively. Heteroduplex mapping and genetic analyses have revealed that the transfer regions are extremely similar between the two plasmids. Plasmid specificity can occur at the level of relaxosome formation, regulation, and surface exclusion between the two transfer systems. There are also differences in pilus serology, pilus-specific phage sensitivity, and requirements for OmpA and lipopolysaccharide components in the recipient cell. These phenotypic differences were exploited in this study to yield new information about the mechanism of pilus synthesis, mating pair stabilization, and surface and/or entry exclusion, which are collectively involved in mating pair formation (Mpf). The sequence of the remainder of the transfer region of R100-1 (trbA to traS) has been completed, and the complete sequence is compared to that of F. The differences between the two transfer regions include insertions and deletions, gene duplications, and mosaicism within genes, although the genes essential for Mpf are conserved in both plasmids. F+ cells carrying defined mutations in each of the Mpf genes were complemented with the homologous genes from R100-1. Our results indicate that the specificity in recipient cell recognition and entry exclusion are mediated by TraN and TraG, respectively, and not by the pilus.     

Naturally occurring plasmids exhibiting incompatibility with members of incompatibility groups I and P

From a group of naturally occurring antibiotic resistance plasmids, a number of plasmids were identified which were incompatible with members of incompatibility group P and also incompatibility group I alpha or I gamma. These plasmids also exhibited strong entry exclusion with members of group P only and showed a host range which resembled that of plasmids of group I rather than those of group P. Segregants of a number of these plasmids appeared to have lost some of the incompatability and/or surface exclusion functions. Studies of nucleic acid homology indicated that these plasmids were very similar to one another. They exhibited 15 to 20% nucleic acid homology with representatives of the I alpha and I gamma groups, yet showed less than 2% homology with the group P plasmid RP4.     

Cloning of an exclusion-determining fragment of the IncI plasmid, R144

By cloning a distinct 8 MDa fragment of the IncI plasmid, R144, in the vector pACYC184, two recombinant plasmids were isolated. In these plasmids, pRAH303 and pRAH308, the inserted fragment was in opposite orientations. Both plasmids when present in a recipient strain caused a conjugation-specific exclusion in crosses with donor cells carrying the IncI plasmid R144. Some derivatives of the recombinant plasmids in which parts were deleted, or in which Tn5 transposons were inserted, appeared to be exclusion negative. Analysis in minicells of the gene products of such plasmids together with those of the original recombinant plasmids revealed that the presence of two proteins, with apparent molecular weights of 13,000 and 19,000 Da could be correlated with the exclusion phenomenon.     

Plasmids for naphthalene biodegradation incompatible with IncP-2 and IncP-7 group plasmids

Fourteen conjugative naphthalene degradative plasmids have been classified by incompatibility. It is shown that the plasmids of IncP-9 group are characterized by the minor entry exclusion, with respect to the R plasmids belonging to IncP-2 or IncP-7 groups. On the other hand, the naphthalene degradative plasmids of incompatibility group P-7 exhibit a markedly pronounced entry exclusion, with respect to the R plasmids of the same incompatibility groups. Two naphthalene degradative plasmids reveal incompatibility with the reference plasmids of two Inc groups (P-2 and P-7). These plasmids control also resistance of bacterial cells to potassium tellurite, which is characteristic of the IncP-2 plasmids. Two other naphthalene degradative plasmids are capable of stable coexistence with the IncP-2, P-7 or P-9 reference plasmids.     

traJ independence in expression of traT on F.

Studies of F plasmids in the same cell as a transfer-repressed IncFII R plasmid showed a 100 to 1,000-fold decrease in transfer and a 75-fold decrease in surface exclusion, but no detectable change was shown in the amount of TraTp synthesized. Moreover, a mutation in traJ on F which caused a 10(4)-fold reduction in transfer caused only a 3.6-fold decrease in TraTp. These two findings suggest that a significant amount of traT expression on F is independent of traJ. Furthermore, we showed, using immunoprecipitation of TraTp, that normal amounts of this protein could be present in the cell without producing normal levels of surface exclusion.     

The evolution of a conjugative plasmid and its ability to increase bacterial fitness

Conjugative plasmids are extra-chromosomal DNA elements that are capable of horizontal transmission and are found in many natural isolated bacteria. Although plasmids may carry beneficial genes to their bacterial host, they may also cause a fitness cost. In this work, we studied the evolution of the R1 plasmid and we found that, in spite of the R1 plasmid conferring an initial cost to its host, after 420 generations the cost disappeared in all five independent evolution experiments. In fact, in two of these five experiments evolved conjugative plasmids actually conferred a fitness advantage to their hosts. Furthermore, the relative fitness of the ancestral clone bearing one of the evolved plasmids is significantly higher than both the plasmid-free ancestral cells and the evolved cells carrying the evolved plasmid. Given that the R1 plasmid may spread among different species of enterobacteria, we wondered what the effect of the evolved plasmid would be inside Salmonella enterica cells. We found that the evolved plasmid is also able to dramatically increase the relative fitness of these cells. Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains.     

Incidence of the H2 group of plasmids in chloramphenicol-sensitive salmonella isolated in 1974 from clinical sources in Ontario.

Chloramphenicol resistance in salmonella obtained from clinical sources in Ontario was previously found to be often mediated by R plasmids of the H2 incompatibility group. In the present study 40 salmonella strains resistant to one or more of kanamycin, streptomycin, sulfonamides, or tetracycline but sensitive to chloramphenicol, were investigated to determine if they contained R plasmids. Self-transmissible plasmids were isolated from 17 of the strains, and 7 of those showed the bacteriophage inhibition and thermosensitive mechanism of transfer characteristic of H2 plasmids. Entry exclusion and incompatibility experiments confiremd their classification. The results demonstrate that in this population of salmonella, R plasmids of the H2 group are prevalent. Experiments with plasmid-specific phages indicate that the plasmids of this sample, which are not in the H2 group, do not belong to any of the F, I, N, P, or W incompatibility groups.     

Cooperation in defence against a predator

The origin and the evolutionary stability of cooperation between unrelated individuals is one of the key problems of evolutionary biology. In this paper, a cooperative defence game against a predator is introduced which is based on Hamilton's selfish herd theory and Eshel's survival game models. Cooperation is altruistic in the sense that the individual, which is not the target of the predator, helps the members of the group attacked by the predator and during defensive action the helper individual may also die in any attack. In order to decrease the long term predation risk, this individual has to carry out a high risk action. Here I show that this kind of cooperative behaviour can evolve in small groups. The reason for the emergence of cooperation is that if the predator does not kill a mate of a cooperative individual, then the survival probability of the cooperative individual will increase in two cases. If the mate is non-cooperative, then—according to the dilution effect, the predator confusion effect and the higher predator vigilance—the survival probability of the cooperative individual increases. The second case is when the mate is cooperative, because a cooperative individual has a further gain, the active help in defence during further predator attacks. Thus, if an individual can increase the survival rate of its mates (no matter whether the mate is cooperative or not), then its own predation risk will decrease.     

The Evolution of Resource Adaptation: How Generalist and Specialist Consumers Evolve

Why and how specialist and generalist strategies evolve are important questions in evolutionary ecology. In this paper, with the method of adaptive dynamics and evolutionary branching, we identify conditions that select for specialist and generalist strategies. Generally, generalist strategies evolve if there is a switching benefit; specialists evolve if there is a switching cost. If the switching cost is large, specialists always evolve. If the switching cost is small, even though the consumer will first evolve toward a generalist strategy, it will eventually branch into two specialists.     

Specific resistance prevents the evolution of general resistance and facilitates disease emergence

Host-shifts, where pathogens jump from an ancestral host to a novel host, can be facilitated or impeded by standing variation in disease resistance, but only if resistance provides broad-spectrum general resistance against multiple pathogen species. Host resistance comes in many forms and includes both general resistance, as well as specific resistance, which may only be effective against a single pathogen species or even genotype. However, most evolutionary models consider only one of these forms of resistance, and we have less understanding of how these two forms of resistance evolve in tandem. Here, we develop a model that allows for the joint evolution of specific and general resistance and asks if the evolution of specific resistance drives a decrease in the evolution of general resistance. We also explore how these evolutionary outcomes affect the risk of foreign pathogen invasion and persistence. We show that in the presence of a single endemic pathogen, the two forms of resistance are strongly exclusionary. Critically, we find that specific resistance polymorphisms can prevent the evolution of general resistance, facilitating the invasion of foreign pathogens. We also show that specific resistance polymorphisms are a necessary condition for the successful establishment of foreign pathogens following invasion, as they prevent the exclusion of the foreign pathogen by the more transmissible endemic pathogen. Our results demonstrate the importance of considering the joint evolution of multiple forms of resistance when evaluating a population's susceptibility to foreign pathogens.     

Fertility inhibition of RP1 by IncN plasmid pKM101.

IncN plasmids, including pKM101, strongly inhibit the conjugal transfer of cohabiting IncP plasmids. We localized the pKM101 DNA sufficient for this phenomenon to a 1.1-kilobase region (denoted fip). Two fip-deficient Tn5 insertion derivatives of pKM101 were isolated; neither affected other pKM101-mediated functions. fip did not inhibit either the synthesis of the IncP plasmid's sex pilus or its ability to mediate entry exclusion against other IncP plasmids.     

Population‐level consequences of risky dispersal

Achieving sufficient connectivity between populations is essential for persistence, but costs of dispersal may select against individual traits or behaviours that, if present, would improve connectivity. Existing dispersal models tend to ignore the multitude of risks to individuals: while many assess the effect of mortality costs, there is also a risk of failing to find new habitat, especially when the entire inhabitable area remains both small and fragmented. There are few known rules governing whether individuals evolve to disperse more, or less, than what is ideal for population connectivity and persistence. Here we aim to fill this gap, while also noting that evolution might not only produce suboptimal dispersal behaviour: it also influences individual heterogeneity in dispersal. Intuitively, we might expect heterogeneity to improve connectivity, as some individuals will travel far. However, we show that this is only true if dispersal distances on average are quite short; heterogeneity can also lead to reduced connectivity because it can reduce the proportion of the most profitable (‘safest’) intermediate dispersal distances. In general, our results show that conditions typically associated with conservation concerns (small and fragmented habitats inhabited by a species with a low birth rate) are also ones that are most likely to lead to suboptimal dispersal traits. This prompts the question of assisted dispersal in cases of urgent conservation concern.