Positive selection and recombination: major molecular mechanisms in colicin diversification

QUORUM SENSING AND GROUP SELECTION

Bacteria respond to cell density by expressing genes whose products are beneficial to the population as a whole. This response is brought about through the release into the medium of signaling molecules of the class N-acyl homoserine lactones, the concentration of which determines the level of gene expression. This form of communication between cells has been termed "quorum sensing," and has been found to operate in the control of many functions in a variety of gram-negative bacteria. As with all signaling between individuals, if fitness costs are associated with the release of and response to the signal, the inclusive fitness of alleles responsible for the phenomenon depends upon genetic relatedness between signaler and responder. The situation is considered in explicit models for bacterial population genetics, in which the critical parameter determining the success of quorum sensing is the mean number of cells founding a population sharing a patch of resource. It is found that extensive polymorphism for the presence or absence of quorum sensing is expected for a wide range of parameter space. If local communities of bacteria contain diverse species, community stability may be the consequence of these interactions rather than polymorphism.

Diversification of β-Augmentation Interactions between CDI Toxin/Immunity Proteins

Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effectors carry diverse C-terminal toxin domains (CdiA-CT), which are delivered into neighboring target cells to inhibit growth. CDI(+) bacteria also produce CdiI immunity proteins that bind specifically to cognate CdiA-CT toxins and protect the cell from auto-inhibition. Here, we compare the structures of homologous CdiA-CT/CdiI complexes from Escherichia coli EC869 and Yersinia pseudotuberculosis YPIII to explore the evolution of CDI toxin/immunity protein interactions. Both complexes share an unusual β-augmentation interaction, in which the toxin domain extends a β-hairpin into the immunity protein to complete a six-stranded anti-parallel sheet. However, the specific contacts differ substantially between the two complexes. The EC869 β-hairpin interacts mainly through direct H-bond and ion-pair interactions, whereas the YPIII β-hairpin pocket contains more hydrophobic contacts and a network of bridging water molecules. In accord with these differences, we find that each CdiI protein only protects target bacteria from its cognate CdiA-CT toxin. The compact β-hairpin binding pocket within the immunity protein represents a tractable system for the rationale design of small molecules to block CdiA-CT/CdiI complex formation. We synthesized a macrocyclic peptide mimic of the β-hairpin from EC869 toxin and solved its structure in complex with cognate immunity protein. These latter studies suggest that small molecules could potentially be used to disrupt CDI toxin/immunity complexes.

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.

Structures of the Ultra-High-Affinity Protein-Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa

How ultra-high-affinity protein-protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase-Im interaction is a model system for the study of high-affinity protein-protein interactions. However, despite the fact that closely related colicin-like bacteriocins are widely produced by Gram-negative bacteria, this interaction has only been studied using colicins from Escherichia coli. In this work, we present the first crystal structures of two pyocin DNase-Im complexes from Pseudomonas aeruginosa, pyocin S2 DNase-ImS2 and pyocin AP41 DNase-ImAP41. These structures represent divergent DNase-Im subfamilies and are important in extending our understanding of protein-protein interactions for this important class of high-affinity protein complex. A key finding of this work is that mutations within the immunity protein binding energy hotspot, helix III, are tolerated by complementary substitutions at the DNase-Immunity protein binding interface. Im helix III is strictly conserved in colicins where an Asp forms polar interactions with the DNase backbone. ImAP41 contains an Asp-to-Gly substitution in helix III and our structures show the role of a co-evolved substitution where Pro in DNase loop 4 occupies the volume vacated and removes the unfulfilled hydrogen bond. We observe the co-evolved mutations in other DNase-Immunity pairs that appear to underpin the split of this family into two distinct groups.

CdiA from Enterobacter cloacae delivers a toxic ribosomal RNase into target bacteria

Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. CDI(+) cells export large CdiA effector proteins, which carry a variety of C-terminal toxin domains (CdiA-CT). CdiA-CT toxins are specifically neutralized by cognate CdiI immunity proteins to protect toxin-producing cells from autoinhibition. Here, we use structure determination to elucidate the activity of a CDI toxin from Enterobacter cloacae (ECL). The structure of CdiA-CT(ECL) resembles the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis. In accord with this structural homology, we show that CdiA-CT(ECL) uses the same nuclease activity to inhibit bacterial growth. Surprisingly, although colicin E3 and CdiA(ECL) carry equivalent toxin domains, the corresponding immunity proteins are unrelated in sequence, structure, and toxin-binding site. Together, these findings reveal unexpected diversity among 16S rRNases and suggest that these nucleases are robust and versatile payloads for a variety of toxin-delivery platforms.

The evolution of restraint in bacterial biofilms under nontransitive competition

Theoretical and empirical evidence indicates that competing species can coexist if dispersal, migration, and competitive interactions occur over relatively small spatial scales. In particular, spatial structure appears to be critical to certain communities with nontransitive competition. A typical nontransitive system involves three competing species that satisfy a relationship similar to the children's game of rock-paper-scissors. Although the ecological dynamics of nontransitive systems in spatially structured communities have received some attention, fewer studies have incorporated evolutionary change. Here we investigate evolution within toxic bacterial biofilms using an agent-based simulation that represents a nontransitive community containing three populations of Escherichia coli. In structured, nontransitive communities, strains evolve that do not maximize their competitive ability: They do not reduce their probability of death to a minimum or increase their toxicity to a maximum. That is, types evolve that exercise restraint. We show that nontransitivity and spatial structure (in the form of localized interactions) are both necessary for the evolution of restraint in these biofilms.

Colicin biology

Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic determinants for colicin synthesis, immunity, and release. Insights gained into each fundamental aspect of their biology are presented: their synthesis, which is under SOS regulation; their release into the extracellular medium, which involves the colicin lysis protein; and their uptake mechanisms and modes of action. Colicins are organized into three domains, each one involved in a different step of the process of killing sensitive bacteria. The structures of some colicins are known at the atomic level and are discussed. Colicins exert their lethal action by first binding to specific receptors, which are outer membrane proteins used for the entry of specific nutrients. They are then translocated through the outer membrane and transit through the periplasm by either the Tol or the TonB system. The components of each system are known, and their implication in the functioning of the system is described. Colicins then reach their lethal target and act either by forming a voltage-dependent channel into the inner membrane or by using their endonuclease activity on DNA, rRNA, or tRNA. The mechanisms of inhibition by specific and cognate immunity proteins are presented. Finally, the use of colicins as laboratory or biotechnological tools and their mode of evolution are discussed.

Relative importance of bacteriocin-like genes in antagonism of Xanthomonas perforans tomato race 3 to Xanthomonas euvesicatoria tomato race 1 strains

In a previous study, tomato race 3 (T3) strains of Xanthomonas perforans became predominant in fields containing both X. euvesicatoria and X. perforans races T1 and T3, respectively. This apparent ability to take over fields led to the discovery that there are three bacteriocin-like compounds associated with T3 strains. T3 strain 91-118 produces at least three different bacteriocin-like compounds (BCN-A, BCN-B, and BCN-C) antagonistic toward T1 strains. We determined the relative importance of the bacteriocin-like compounds by constructing the following mutant forms of a wild-type (WT) T3 strain to evaluate the antagonism to WT T1 strains: Mut-A (BCN-A-), Mut-B (BCN-B-), Mut-C (BCN-C-), Mut-AB, Mut-BC, and Mut-ABC. Although all mutant and WT T3 strains reduced the T1 populations in in planta growth room experiments, Mut-B and WT T3 were significantly more effective. Mutants expressing BCN-B and either BCN-A or BCN-C reduced T1 populations less than mutants expressing only BCN-A or BCN-C. The triple-knockout mutant Mut-ABC also had a significant competitive advantage over the T1 strain. In pairwise-inoculation field experiments where plants were coinoculated with an individual mutant or WT T3 strain and the T1 strain, the mutant strains and the WT T3 strain were reisolated from more than 70% of the lesions. WT T3 and Mut-B were the most frequently reisolated strains. In field experiments where plants were group inoculated with Mut-A, Mut-B, Mut-C, Mut-ABC, and WT T1 and T3 strains, Mut-B populations dominated all three seasons. In greenhouse and field experiments, the WT and mutant T3 strains had a selective advantage over T1 strains. Bacterial strains expressing both BCN-A and BCN-C appeared to have a competitive advantage over all other mutant and WT strains. Furthermore, BCN-B appeared to be a negative factor, with mutant T3 strains lacking BCN-B having a selective advantage in the field.

Chimeric nature of two plasmids of Hafnia alvei encoding the bacteriocins alveicins A and B

The complete nucleotide sequences of two bacteriocin-encoding plasmids isolated from Hafnia alvei (pAlvA and pAlvB) were determined. Both plasmids resemble ColE1-type replicons and carry mobilization genes, as well as colicin-like bacteriocin operons. These bacteriocins appear to be chimeras consisting of translocation domains from Tol-dependent colicins, unique binding domains, and killing and immunity domains similar to those of the pore-forming colicin Ia. Just as is found for colicin Ia, these H. alvei bacteriocins (alveicins) lack lysis genes. The alveicins are unusually small at 408 and 358 amino acids for alveicin A and B, respectively, which would make alveicin B the smallest pore-forming bacteriocin yet discovered. The pattern of nucleotide substitution in the alveicins suggests that the dominant forces in the evolution of their killing domains and immunity genes are neutral mutation and random genetic drift rather than diversifying selection, which has been implicated in the evolution of other colicins. Five of six bacteriocinogenic isolates of H. alvei were found to carry plasmids identical to pAlvA. Comparisons of the levels of nucleotide divergence in five housekeeping genes to the levels of divergence in their respective plasmids led us to conclude that pAlvA is transferring laterally through the H. alvei population relatively rapidly.

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.

Bacteriocin diversity: ecological and evolutionary perspectives

The bacteriocin family is the most abundant and diverse group of bacterial defense systems. Bacteriocins range from the well-studied narrow spectrum, high molecular weight colicins produced by Escherichia coli and the short polypeptide lantibiotics of lactic acid bacteria to the relatively unknown halocins produced almost universally by the haolobacteria. The abundance and diversity of this potent arsenal of weapons is clear. Less clear is 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 best-characterized family of bacteriocins, the colicins. 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.

Chemical warfare between microbes promotes biodiversity

Evolutionary processes generating biodiversity and ecological mechanisms maintaining biodiversity seem to be diverse themselves. Conventional explanations of biodiversity such as niche differentiation, density-dependent predation pressure, or habitat heterogeneity seem satisfactory to explain diversity in communities of macrobial organisms such as higher plants and animals. For a long time the often high diversity among microscopic organisms in seemingly uniform environments, the famous "paradox of the plankton," has been difficult to understand. The biodiversity in bacterial communities has been shown to be sometimes orders of magnitudes higher than the diversity of known macrobial systems. Based on a spatially explicit game theoretical model with multiply cyclic dominance structures, we suggest that antibiotic interactions within microbial communities may be very effective in maintaining diversity.

The molecular evolution of signal peptides

Signal peptides direct mature peptides to their appropriate cellular location, after which they are cleaved off. Very many random alternatives can serve the same function. Of all coding sequences, therefore, signal peptides might come closest to being neutrally evolving. Here we consider this issue by examining the molecular evolution of 76 mouse-rat orthologues, each with defined signal peptides. Although they do evolve rapidly, they evolve about half as fast as neutral sequences. This indicates that a substantial proportion of mutations must be under stabilizing selection. A few putative signal sequences lack a hydrophobic core and these tend to be more slowly evolving than others, indicating even stronger stabilizing selection. However, closer scrutiny suggests that some of these represent mis-annotations in GenBank. It is also likely that some of the substitutions are not neutral. We find, for example, that the rate of protein evolution correlates with that of the mature peptide. This may be a result of compensatory evolution. We also find that signal peptides of immune genes tend to be faster evolving than the average, which suggests an association with antagonistic co-evolution. Previous reports also indicated that the signal peptide of the imprinted gene, Igf2r, is also unusually fast evolving. This, it was hypothesized, might also be indicative of antagonistic co-evolution. Comparison of Igf2r's signal peptide evolution shows that, although it is not an outlier, its rate of evolution is comparable to that of many of the faster evolving immune system signal sequences and 5/6 of the amino acid changes do not conserve hydrophobicity. This is at least suggestive that there is something unusual about Igf2r's signal sequence.

The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification

Two evolutionary mechanisms have been proposed in the process of protein diversification of the large family of antimicrobial toxins of Escherichia coli, known as the colicins. Data from previous studies suggest that the relatively rare nuclease colicins appear to diversify primarily through the action of positive selection, whilst the more abundant pore-former colicins appear to diversify through the action of recombination. The complete DNA sequence of the newly characterized colicin plasmid, pCol-Let, isolated from a Yanomama Indian of South America, is presented here. This plasmid encodes a newly identified pore-former colicin, colicin Y. DNA and protein sequence comparisons of the colicin Y gene cluster and the encoded proteins with those of published pore-former colicins provide the first evidence that positive selection may also act to increase pore-former colicin diversity.

Competition by allelopathy proceeds in traveling waves: colicin-immune strain aids colicin-sensitive strain

Producing toxic chemicals to suppress both the growth and survivorship of local competitors is called allelopathy; some strains of the bacteria Escherichia coli produce a toxin (named colicin) which may kill colicin-sensitive neighbors while they themselves are immune. In a previous paper, the competitive outcome between colicin-producing and colicin-sensitive strains was shown to differ between a spatially structured and a completely mixed population. In this paper, we analyze the role of a third, "colicin-immune," strain, which does not produce colicin but is immune to it. Without spatial structure, the colicin-immune strain suppresses the colicin-producing strain and enables the colicin-sensitive strain to win. In a spatially structured population, modeled as a reaction-diffusion system, we examine the speed of boundaries between areas dominated by different strains in traveling waves and the events after the collision of two such boundaries. The colicin-immune strain passes through the area dominated by the colicin-sensitive strain and drives the colicin-producing strain to extinction. Subsequently the colicin-sensitive strain occupies the whole population.

The ecological role of bacteriocins in bacterial competition

Bacteriocins are an abundant class of antimicrobial molecules that appear to mediate population dynamics within species. The bacteriocins of Escherichia coli have served as a model for exploring the ecological role of these potent toxins. Studies suggest that colicins provide a competitive edge in nutrient-poor environments and that there might be a trade-off between the costs and benefits of colicin production.

Molecular mechanisms of bacteriocin evolution

Microorganisms are engaged in a never-ending arms race. One consequence of this intense competition is the diversity of antimicrobial compounds that most species of bacteria produce. Surprisingly, little attention has been paid to the evolution of such extraordinary diversity. One class of antimicrobials, the bacteriocins, has received increasing attention because of the high levels of bacteriocin diversity observed and the use of bacteriocins as preservatives in the food industry and as antibiotics in the human health industry. However, little effort has been focused on evolutionary questions, such as what are the phylogenetic relationships among these toxins, what mechanisms are involved in their evolution, and how do microorganisms respond to such an arsenal of weapons? The focus of this review is to provide a detailed picture of our current understanding of the molecular mechanisms involved in the process of bacteriocin diversification.

Do we understand the evolution of genomic imprinting?

The conflict theory is the only hypothesis to have attracted any critical attention for the evolution of genomic imprinting. Although the earliest data appeared supportive, recent systematic analyses have not confirmed the model's predictions. The status of theory remains undecided, however, as post-hoc explanations can be provided as to why these predictions are not borne out.

Sex and conflict

Evolutionary conflict occurs when the deterministic spread of an allele lowers the fitness either of its bearer or of other individuals in the population, leading to selection for suppressors. Sex promotes conflict because associations between alleles are temporary. Differing selection on males and females, sexual selection, and differences in transmission patterns between classes of nuclear and cytoplasmic genes can all give rise to conflict. Inert Y chromosomes, uniparental inheritance of cytoplasmic genes, mating strains and sexes, and many features of sexual behavior may have evolved in part as a result of evolutionary conflict. Estimates of its quantitative importance, however, are still needed.