Signal diffusion and the mitigation of social exploitation in pneumococcal competence signalling

The pneumococcal social network

Gram-positive bacteria employ an array of secreted peptides to control population-level behaviors in response to environmental cues. We review mechanistic and functional features of secreted peptides produced by the human pathogen Streptococcus pneumoniae. We discuss sequence features, mechanisms of transport, and receptors for 3 major categories of small peptides: the double-glycine peptides, the Rap, Rgg, NprR, PlcR, and PrgX (RRNPP)-binding peptides, and the lanthionine-containing peptides. We highlight the impact of factors that contribute to carriage and pathogenesis, specifically genetic diversity, microbial competition, biofilm development, and environmental adaptation. A recent expansion in pneumococcal peptide studies reveals a complex network of interacting signaling systems where multiple peptides are integrated into the same signaling pathway, allowing multiple points of entry into the pathway and extending information content in new directions. In addition, since peptides are present in the extracellular milieu, there are opportunities for crosstalk, quorum sensing (QS), as well as intra- and interstrain and species interactions. Knowledge on the manner that population-level behaviors contribute to disease provides an avenue for the design and development of anti-infective strategies.

Discovery, development and exploitation of steady-state biofilms

Early in vitro biofilm models go back even beyond the invention of the word 'biofilm'. In the dental field, biofilms were simply known as dental plaque and many of the first in vitro models were termed 'artificial mouth microcosm plaques'. The purpose of this review is to highlight important elements of research from over the years regarding in vitro biofilm models, including data from our own laboratories. This helps us to interpret the models and point the way to the future development of biofilm testing. Many hypotheses regarding biofilm phenomena, particularly ecology, metabolism and physiology of volatile sulphur compounds (VSCs) and volatile organic compound (VOC) production could potentially be supported or disproved. In this way, the methods we use for screening biologically active agents including inhibitors, biocides and antimicrobial compounds in general can be improved. Hopefully, any lessons learnt in the past may be of value for the future. In this review, we focus around the need for growth rate controlled long-term biofilms; being continuously monitored using recent technical advances in bioluminescence, selective real-time electrodes, pH electrodes and continuous on-line analysis of the gas phase (both qualitatively and quantitatively). These features allow for accurate determination of growth rate and/or metabolic rate as well as pave the way towards automated assays and fine control of metabolism; impossible to achieve according to conventional biofilm theory. We also attempt to address the questions; can biofilm systems be improved to maintain long term 'real' or 'true' steady states over weeks or months, or are we limited to quasi-steady state systems for a limited period of time.

Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production in Streptococcus pneumoniae

Quorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion in Streptococcus pneumoniae, encoded by the blp operon (bacteriocin-like peptide). Analysis of 4096 pneumococcal genomes detected nine blp QS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmed in vitro by measuring the response of reporter strains containing six different blp QS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.

Steady at the wheel: conservative sex and the benefits of bacterial transformation

Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence

Streptococcus pneumoniae becomes competent for genetic transformation when exposed to an autoinducer peptide known as competence-stimulating peptide (CSP). This peptide was originally described as a quorum-sensing signal, enabling individual cells to regulate competence in response to population density. However, recent studies suggest that CSP may instead serve as a probe for sensing environmental cues, such as antibiotic stress or environmental diffusion. Here, we show that competence induction can be simultaneously influenced by cell density, external pH, antibiotic-induced stress, and cell history. Our experimental data is explained by a mathematical model where the environment and cell history modify the rate at which cells produce or sense CSP. Taken together, model and experiments indicate that autoinducer concentration can function as an indicator of cell density across environmental conditions, while also incorporating information on environmental factors or cell history, allowing cells to integrate cues such as antibiotic stress into their quorum-sensing response. This unifying perspective may apply to other debated quorum-sensing systems.

Peptide CSP regulates natural competence in pneumococci and has been proposed as a quorum-sensing signal or a probe for sensing environmental cues. Here, the authors show that CSP levels can indeed act as an indicator of cell density and also incorporate information on environmental factors or cell history.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System

A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Sponge-Inspired Dibromohemibastadin Prevents and Disrupts Bacterial Biofilms without Toxicity

Since the banning of several families of compounds in antifouling (AF) coatings, the search for environmentally friendly AF compounds has intensified. Natural sources of AF compounds have been identified in marine organisms and can be used to create analogues in laboratory. In a previous study, we identified that dibromohemibastadin-1 (DBHB) is a promising AF molecule, leading to the inhibition of the activity of phenoloxidase, an enzyme involved in the attachment of mussels to surfaces. This paper describes the activity of the DBHB on biofilm formation and its detachment and on bacterial adhesion and communication: quorum sensing. DBHB has an anti-biofilm activity without affecting adhesion of marine and terrestrial bacteria at a dose of 10 µM. Moreover, DBHB activity on quorum sensing (QS) is demonstrated at doses of 8 and 16 µM. The activity of DBHB on QS is compared to kojic acid, a quorum sensing inhibitor already described. This compound is a promising environmentally friendly molecule potentially useful for the inhibition of microfouling.

Diversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of Pseudomonas aeruginosa Infecting Cystic Fibrosis Lungs

Type II toxin-antitoxin (TA) systems are most commonly composed of two genes encoding a stable toxin, which harms the cell, and an unstable antitoxin that can inactivate it. TA systems were initially characterized as selfish elements, but have recently gained attention for regulating general stress responses responsible for pathogen virulence, formation of drug-tolerant persister cells and biofilms—all implicated in causing recalcitrant chronic infections. We use a bioinformatics approach to explore the distribution and evolution of type II TA loci of the opportunistic pathogen, Pseudomonas aeruginosa, across longitudinally sampled isolates from cystic fibrosis lungs. We identify their location in the genome, mutations, and gain/loss during infection to elucidate their function(s) in stabilizing selfish elements and pathogenesis. We found (1) 26 distinct TA systems, where all isolates harbor four in their core genome and a variable number of the remaining 22 on genomic islands; (2) limited mutations in core genome TA loci, suggesting they are not under negative selection; (3) no evidence for horizontal transmission of elements with TA systems between clone types within patients, despite their ability to mobilize; (4) no gain and limited loss of TA-bearing genomic islands, and of those elements partially lost, the remnant regions carry the TA systems supporting their role in genomic stabilization; (5) no significant correlation between frequency of TA systems and strain ability to establish as chronic infection, but those with a particular TA, are more successful in establishing a chronic infection.

Cheating fosters species co-existence in well-mixed bacterial communities

Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats. Using experimental communities consisting of the strong competitor Pseudomonas aeruginosa (PA) and its weaker counterpart Burkholderia cenocepacia (BC), we show that co-existence is impossible when the two species compete for a single limiting resource, iron. However, when introducing a PA cheating mutant, which specifically exploits the iron-scavenging siderophores produced by the PA wild type, we found that biodiversity was preserved under well-mixed conditions where PA cheats could outcompete the PA wild type. Cheating fosters biodiversity in our system because it creates strong intra-specific competition, which equalizes fitness differences between PA and BC. Our study identifies cheating - typically considered a destructive element - as a constructive force in shaping biodiversity.

Pneumococcal Competence Coordination Relies on a Cell-Contact Sensing Mechanism

Bacteria have evolved various inducible genetic programs to face many types of stress that challenge their growth and survival. Competence is one such program. It enables genetic transformation, a major horizontal gene transfer process. Competence development in liquid cultures of Streptococcus pneumoniae is synchronized within the whole cell population. This collective behavior is known to depend on an exported signaling Competence Stimulating Peptide (CSP), whose action generates a positive feedback loop. However, it is unclear how this CSP-dependent population switch is coordinated. By monitoring spontaneous competence development in real time during growth of four distinct pneumococcal lineages, we have found that competence shift in the population relies on a self-activated cell fraction that arises via a growth time-dependent mechanism. We demonstrate that CSP remains bound to cells during this event, and conclude that the rate of competence development corresponds to the propagation of competence by contact between activated and quiescent cells. We validated this two-step cell-contact sensing mechanism by measuring competence development during co-cultivation of strains with altered capacity to produce or respond to CSP. Finally, we found that the membrane protein ComD retains the CSP, limiting its free diffusion in the medium. We propose that competence initiator cells originate stochastically in response to stress, to form a distinct subpopulation that then transmits the CSP by cell-cell contact.

Development of competence for genetic transformation by cultures of pneumococcal cells has been considered till now as a classic example of quorum sensing, whereby a culture attaining a sufficient cell density detects a diffusible signaling molecule (in this case, Competence-Stimulating Peptide (CSP)) and switches en masse to a distinct physiological state. We find that the competence shift is dictated not by cell density but by growth for a time allowing emergence of a competence-initiator sub-population, and spreads by transmission of CSP through cell contact. This behaviour reflects the survival benefits of allowing subsets of the population to respond to environmental stress by generating signalling capacity, which prepares the entire population for a rapid and appropriate response to threatening conditions.

Peptide conversations in Gram-positive bacteria

Within Gram-positive bacteria, the expression of target genes is controlled at the population level via signaling peptides, also known as pheromones. Pheromones control a wide range of functions, including competence, virulence, and others that remain unknown. Until now, their role in bacterial gene regulation has probably been underestimated; indeed, bacteria are able to produce, by ribosomal synthesis or surface protein degradation, an extraordinary variety of peptides which are released outside bacteria and among which, some are pheromones that mediate cell-to-cell communication. The review aims at giving an updated overview of these peptide-dependant communication pathways. More specifically, it follows the whole peptide circuit from the peptide production and secretion in the extracellular medium to its interaction with sensors at bacterial surface or re-import into the bacteria where it plays its regulation role. In recent years, as we have accumulated more knowledge about these systems, it has become apparent that they are more complex than they first appeared. For this reason, more research on peptide-dependant pathways is needed to develop new strategies for controlling functions of interest in Gram-positive bacteria. In particular, such research could lead to alternatives to the use of antibiotics against pathogenic bacteria. In perspective, the review identifies new research questions that emerge in this field and that have to be addressed.

Cooperation, quorum sensing, and evolution of virulence in Staphylococcus aureus

The virulence and fitness in vivo of the major human pathogen Staphylococcus aureus are associated with a cell-to-cell signaling mechanism known as quorum sensing (QS). QS coordinates the production of virulence factors via the production and sensing of autoinducing peptide (AIP) signal molecules by the agr locus. Here we show, in a wax moth larva virulence model, that (i) QS in S. aureus is a cooperative social trait that provides a benefit to the local population of cells, (ii) agr mutants, which do not produce or respond to QS signal, are able to exploit the benefits provided by the QS of others ("cheat"), allowing them to increase in frequency when in mixed populations with cooperators, (iii) these social interactions between cells determine virulence, with the host mortality rate being negatively correlated to the percentage of agr mutants ("cheats") in a population, and (iv) a higher within-host relatedness (lower strain diversity) selects for QS and hence higher virulence. Our results provide an explanation for why agr mutants show reduced virulence in animal models but can be isolated from infections of humans. More generally, by providing the first evidence that QS is a cooperative social behavior in a Gram-positive bacterium, our results suggest convergent, and potentially widespread, evolution for signaling to coordinate cooperation in bacteria.

[Quorum sensing in bacteria and yeast]

Bacterial sets are complex dynamic systems, which interact with each other and through the interaction, bacteria coexist, collaborate, compete and share information in a coordinated manner. A way of bacterial communication is quorum sensing. Through this mechanism the bacteria can recognize its concentration in a given environment and they can decide the time at which the expression of a particular set of genes should be started for developing a specific and simultaneous response. The result of these interconnections raises properties that cannot be explained from a single isolated bacterial cell.

Toward an evolutionary definition of cheating

The term "cheating" is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term "cheat" from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.

Significant variation in transformation frequency in Streptococcus pneumoniae

The naturally transformable bacterium Streptococcus pneumoniae is able to take up extracellular DNA and incorporate it into its genome. Maintaining natural transformation within a species requires that the benefits of transformation outweigh its costs. Although much is known about the distribution of natural transformation among bacterial species, little is known about the degree to which transformation frequencies vary within species. Here we find that there is significant variation in transformation frequency between strains of Streptococcus pneumoniae isolated from asymptomatic carriage, and that this variation is not concordant with isolate genetic relatedness. Polymorphism in the signalling system regulating competence is also not causally related to differences in transformation frequency, although this polymorphism does influence the degree of genetic admixture experienced by bacterial strains. These data suggest that bacteria can evolve new transformation frequencies over short evolutionary timescales. This facility may permit cells to balance the potential costs and benefits of transformation by regulating transformation frequency in response to environmental conditions.

Quorum sensing and the confusion about diffusion

Two hypotheses, termed quorum sensing (QS) and diffusion sensing (DS), have been suggested as competing explanations for why bacterial cells use the local concentration of small molecules to regulate numerous extracellular behaviours. Here, we show that: (i) although there are important differences between QS and DS, they are not diametrically opposed; (ii) empirical attempts to distinguish between QS and DS are misguided and will lead to confusion; (iii) the fundamental distinction is not between QS and DS, but whether or not the trait being examined is social; (iv) empirical data are consistent with both social interactions and a role of diffusion; (v) alternate hypotheses, such as efficiency sensing (ES), are not required to unite QS and DS. More generally, work in this area illustrates how the use of jargon can obscure the underlying concepts and key questions.

Competence in Streptococcus pneumoniae is regulated by the rate of ribosomal decoding errors

Competence for genetic transformation in Streptococcus pneumoniae develops in response to accumulation of a secreted peptide pheromone and was one of the initial examples of bacterial quorum sensing. Activation of this signaling system induces not only expression of the proteins required for transformation but also the production of cellular chaperones and proteases. We have shown here that activity of this pathway is sensitively responsive to changes in the accuracy of protein synthesis that are triggered by either mutations in ribosomal proteins or exposure to antibiotics. Increasing the error rate during ribosomal decoding promoted competence, while reducing the error rate below the baseline level repressed the development of both spontaneous and antibiotic-induced competence. This pattern of regulation was promoted by the bacterial HtrA serine protease. Analysis of strains with the htrA (S234A) catalytic site mutation showed that the proteolytic activity of HtrA selectively repressed competence when translational fidelity was high but not when accuracy was low. These findings redefine the pneumococcal competence pathway as a response to errors during protein synthesis. This response has the capacity to address the immediate challenge of misfolded proteins through production of chaperones and proteases and may also be able to address, through genetic exchange, upstream coding errors that cause intrinsic protein folding defects. The competence pathway may thereby represent a strategy for dealing with lesions that impair proper protein coding and for maintaining the coding integrity of the genome.

IMPORTANCE

The signaling pathway that governs competence in the human respiratory tract pathogen Streptococcus pneumoniae regulates both genetic transformation and the production of cellular chaperones and proteases. The current study shows that this pathway is sensitively controlled in response to changes in the accuracy of protein synthesis. Increasing the error rate during ribosomal decoding induced competence, while decreasing the error rate repressed competence. This pattern of regulation was promoted by the HtrA protease, which selectively repressed competence when translational fidelity was high but not when accuracy was low. Our findings demonstrate that this organism is able to monitor the accuracy of information used for protein biosynthesis and suggest that errors trigger a response addressing both the immediate challenge of misfolded proteins and, through genetic exchange, upstream coding errors that may underlie protein folding defects. This pathway may represent an evolutionary strategy for maintaining the coding integrity of the genome.

Spontaneous Gac mutants of Pseudomonas biological control strains: cheaters or mutualists?

Bacteria rely on a range of extracellular metabolites to suppress competitors, gain access to resources, and exploit plant or animal hosts. The GacS/GacA two-component regulatory system positively controls the expression of many of these beneficial external products in pseudomonad bacteria. Natural populations often contain variants with defective Gac systems that do not produce most external products. These mutants benefit from a decreased metabolic load but do not appear to displace the wild type in nature. How could natural selection maintain the wild type in the presence of a mutant with enhanced growth? One hypothesis is that Gac mutants are "cheaters" that do not contribute to the public good, favored within groups but selected against between groups, as groups containing more mutants lose access to ecologically important external products. An alternative hypothesis is that Gac mutants have a mutualistic interaction with the wild type, so that each variant benefits by the presence of the other. In the biocontrol bacterium Pseudomonas chlororaphis strain 30-84, Gac mutants do not produce phenazines, which suppress competitor growth and are critical for biofilm formation. Here, we test the predictions of these alternative hypotheses by quantifying interactions between the wild type and the phenazine- and biofilm-deficient Gac mutant within growing biofilms. We find evidence that the wild type and Gac mutants interact mutualistically in the biofilm context, whereas a phenazine-defective structural mutant does not. Our results suggest that the persistence of alternative Gac phenotypes may be due to the stabilizing role of local mutualistic interactions.

Competence increases survival during stress in Streptococcus pneumoniae

Horizontal gene transfer mediated by transformation is of central importance in bacterial evolution. However, numerous questions remain about the maintenance of processes that underlie transformation. Most hypotheses for the benefits of transformation focus on what bacteria might do with DNA, but ignore the important fact that transformation is subsumed within the broader process of competence. Accordingly, the apparent benefits of transformation might rely less on recombination than on other potential benefits associated with the broader suite of traits regulated by competence. We examined the importance of this distinction in the naturally competent species Streptococcus pneumoniae, focusing specifically on predictions of the DNA-for-repair hypothesis. We confirm earlier results in other naturally competent species that transformation protects against DNA-damaging stress. In addition, we show that the stress-protection extends to non-DNA-damaging stress. More important, we find that for some forms of stress transformation is not required for cells to benefit from the induction of competence. This rejects the narrowly defined DNA-for-repair hypotheses and provides the first support for Claverys' hypothesis that competence, but not necessarily transformation, may act as a general process to relieve stress. Our results highlight the need to distinguish benefits of transformation from broader benefits of competence that do not rely on DNA uptake and recombination.

The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility

Why is motility so common in bacteria? An obvious answer to this ecological and evolutionary question is that in almost all habitats, bacteria need to go someplace and particularly in the direction of food. Although the machinery required for motility and chemotaxis (acquiring and processing the information needed to direct movement toward nutrients) are functionally coupled in contemporary bacteria, they are coded for by different sets of genes. Moreover, information that resources are more abundant elsewhere in a habitat would be of no value to a bacterium unless it already had the means to get there. Thus, motility must have evolved before chemotaxis, and bacteria with flagella and other machinery for propulsion in random directions must have an advantage over bacteria relegated to moving at the whim of external forces alone. However, what are the selection pressures responsible for the evolution and maintenance of undirected motility in bacteria? Here we use a combination of mathematical modeling and experiments with Escherichia coli to generate and test a parsimonious and ecologically general hypothesis for the existence of undirected motility in bacteria: it enables bacteria to move away from each other and thereby obtain greater individual shares of resources in physically structured environments. The results of our experiments not only support this hypothesis, but are quantitatively and qualitatively consistent with the predictions of our model.

Dynamics in the mixed microbial concourse

Isolated, clonal populations of cells are rarely found in nature. The emergent properties of microbial consortia present a challenge for the systems approach to biology, as chances for competition, communication, or collaboration multiply with the number of interacting agents. This review focuses on recent work on intercourse within biofilms, among quorum-sensing populations, and between cross-feeding metabolic cooperators. New tools from synthetic biology allow microbial interactions to be designed and tightly controlled, creating valuable model systems. We address both natural and synthetic partnerships, with an emphasis on how system behaviors derive from the properties of their components. Essential features of microbial biology arose in the context of a very mixed culture and cannot be understood without unscrambling it.