Cell shape,division and development: the 2002 American Society for Microbiology (ASM) conference on prokaryotic development

In the last decade, the use of cytological techniques, together with the analysis of complete genomes, has dramatically advanced our understanding of bacterial development. Work on several well-developed model systems such as Bacillus subtilis, Caulobacter crescentus, Myxococcus xanthus and Streptomyces spp., has provided us with an in-depth understanding of processes such as sporulation, multicellular behaviour and the bacterial cell cycle. At the same time, these studies have revolutionized our view of the bacterial cell and shown it to be a highly complex entity with spatial and temporal organization. The recent American Society for Microbiology (ASM) conference on prokaryotic development demonstrated that several laboratories have now started to connect data obtained through functional genomic analysis with subcellular organization, thereby generating three-dimensional regulatory networks. This meeting report highlights new findings in the field, such as regulation of protein localization during sporulation and the cell cycle, control of cell-cell interaction and the initiation of cell division.     

Development of a dynamic continuous-discrete-continuous model describing the lag phase of individual bacterial cells

AIMS: A previous model for adaptation and growth of individual bacterial cells was not dynamic in the lag phase, and could not be used to perform simulations of growth under non-isothermal conditions. The aim of the present study was to advance this model by adding a continuous adaptation step, prior to the discrete step, to form a continuous-discrete-continuous (CDC) model. METHODS AND RESULTS: The revised model uses four parameters: N(0), initial population; N(max), maximum population; p0, mean initial individual cell physiological state; SD(p0), standard deviation of the distribution of individual physiological states. A truncated normal distribution was used to generate tables of distributions to allow fitting of the CDC model to viable count data for Listeria monocytogenes grown at 5 degrees C to 35 degrees C. The p0 values increased with increasing SD(p0) and were, on average, greater than the corresponding population physiological states (h0); p0 and h0 were equivalent for individual cells. CONCLUSION: The CDC model has improved the ability to simulate the behaviour of individual bacterial cells by using a physiological state parameter and a distribution function to handle inter-cell variability. The stages of development of this model indicate the importance of physiological state parameters over the population lag concept, and provide a potential approach for making growth models more mechanistic by incorporating actual physiological events. SIGNIFICANCE AND IMPACT OF THE STUDY: Individual cell behaviour is important in modelling bacterial growth in foods. The CDC model provides a means of improving existing growth models, and increases the value of mathematical modelling to the food industry.     

Bacterial stationary-state mutagenesis and Mammalian tumorigenesis as stress-induced cellular adaptations and the role of epigenetics

Mechanisms of cellular adaptation may have some commonalities across different organisms. Revealing these common mechanisms may provide insight in the organismal level of adaptation and suggest solutions to important problems related to the adaptation. An increased rate of mutations, referred as the mutator phenotype, and beneficial nature of these mutations are common features of the bacterial stationary-state mutagenesis and of the tumorigenic transformations in mammalian cells. We argue that these commonalities of mammalian and bacterial cells result from their stress-induced adaptation that may be described in terms of a common model. Specifically, in both organisms the mutator phenotype is activated in a subpopulation of proliferating stressed cells as a strategy to survival. This strategy is an alternative to other survival strategies, such as senescence and programmed cell death, which are also activated in the stressed cells by different subpopulations. Sustained stress-related proliferative signalling and epigenetic mechanisms play a decisive role in the choice of the mutator phenotype survival strategy in the cells. They reprogram cellular functions by epigenetic silencing of cell-cycle inhibitors, DNA repair, programmed cell death, and by activation of repetitive DNA elements. This reprogramming leads to the mutator phenotype that is implemented by error-prone cell divisions with the involvement of Y family polymerases. Studies supporting the proposed model of stress-induced cellular adaptation are discussed. Cellular mechanisms involved in the bacterial stress-induced adaptation are considered in more detail.     

Bacterial cyclostatin, or how do bacteria manipulate the eukaryotic cell cycle

Several bacterial proteins have been recently described that share the ability to inhibit the proliferation of cells in culture without causing early signs of cytotoxicity. Such observations suggest the existence of bacterial mechanisms of control of the eukaryotic cell cycle contributing to pathogenicity or adaptation to the host. This emerging concept of cellular microbiology is critically analyzed considering as a model the cytolethal distending toxins (CDT), a family of toxins whose mode of action on the cell cycle has been thoroughly studied over the last few years. CDTs activate a physiological G2 checkpoint in exposed cells, probably from an initial DNA alteration whose precise molecular nature has not yet been determined. Experimental data are lacking to extrapolate in vivo the antiproliferative effect of these bacterial proteins that we tentatively propose to call cyclostatins.     

Immunoreceptors: evolution,structure and therapeutic applications

The ‘Immunoreceptors’ meeting took place in July 2012 in beautiful Snowmass Village in Colorado, USA. At an altitude of more than two kilometres, researchers and clinicians discussed the molecular aspects of immunoreceptors, ranging from B‐ and T‐cell receptors, to complement and Fc receptors.     

The origin and evolution of human pathogens

What are the genetic origins of human pathogens? An international group of scientists discussed this topic at a workshop that took place in late October 2004 in Baeza (Spain). Focusing primarily on bacterial pathogens, they examined the role that pathogenicity islands and bacteriophages play on determining the virulence properties that distinguish closely related members of a given species, such as host range and tissue specificity. They also discussed an instance in which closely related bacterial species differ in the production of a cell surface modification mediating resistance to an antibiotic as a result of the disparate regulation of homologous genes. In certain pathogens, genes normally carrying out housekeeping functions may adopt new functions, whereas in other organisms, genes that respond to stresses associated with non-host environments are silenced during infection to prevent the expression of products that interfere with the normal colonization process. The adaptive behaviour of certain pathogens relies on gene variation at certain loci that by virtue of containing polymeric repeats in regulatory or coding regions, can generate variants that may or may not express products that modify the cell surface of the organism. The meeting also addressed the properties of ORFan genes, which have no homologues in the sequence databases, as well as the creation of genes de novo by duplication and divergence.     

International Helgoland Symposium “Ecosystem research”: Summary,conclusions and closing

This final contribution to the International Helgoland Symposium 1976 summarizes important information presented during the meeting, discusses some concepts and principles of ecosystem research, draws a few conclusions and offers some theories and speculations. It is suggested that, in the future, more attention be payed to: the role of microorganisms for overall system dynamics and for providing trophic and biochemical linkages; behaviour as a regulating factor, especially at higher trophic levels; development of new techniques for operating experimental ecosystems; and critical application of mathematical models. Various functional states of ecosystems are considered in some detail, as are the foodweb concept and system integration. The forces which could contribute to ecosystem integration appear to include non-genetic nutritional adaptation, non-genetic behavioural adaptation, social dynamics and biochemical interactions.     

Entry of OpaA+ gonococci into HEp-2 cells requires concerted action of glycosaminoglycans, fibronectin and integrin receptors

Heparan sulphate proteoglycans are increasingly implicated as eukaryotic cell surface receptors for bacterial pathogens. Here, we report that Neisseria gonorrhoeae adheres to proteoglycan receptors on HEp-2 epithelial cells but that internalization of the bacterium by this cell type requires the serum glycoprotein fibronectin. Fibronectin was shown to bind specifically to gonococci producing the OpaA adhesin. Binding assays with fibronectin fragments located the bacterial binding site near the N-terminal end of the molecule. However, none of the tested fibronectin fragments supported gonococcal entry into the eukaryotic cells; a 120 kDa fragment carrying the cell adhesion domain with the amino acid sequence RGD even inhibited the fibronectin-mediated uptake of MS11-OpaA. This inhibition could be mimicked by an RGD-containing hexapeptide and by α5β1 integrin-specific antibodies, suggesting that interaction of the central region of fibronectin with integrin receptors facilitated bacterial uptake. Fibronectin was unable to promote gonococcal entry into HEp-2 cells that had been treated with the enzyme heparinase III, which degrades the glycosaminoglycan side-chains of proteoglycan receptors. On the basis of these results, we propose a novel cellular uptake pathway for bacteria, which involves the binding of the pathogen to glycosaminoglycans that, in turn, act as co-receptors facilitating fibronectin-mediated bacterial uptake through integrin receptors. In this scenario, fibronectin would act as a molecular bridge linking the Opa–proteoglycan complex with host cell integrin receptors.     

Travelling Waves in Hybrid Chemotaxis Models

Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are investigated. Bacteria are modelled using an agent-based (individual-based) approach with internal dynamics describing signal transduction. In addition to the chemotactic behaviour of the bacteria, the individual-based model also includes cell proliferation and death. Cells consume the extracellular nutrient field (chemoattractant), which is modelled using a partial differential equation. Mesoscopic and macroscopic equations representing the behaviour of the hybrid model are derived and the existence of travelling wave solutions for these models is established. It is shown that cell proliferation is necessary for the existence of non-transient (stationary) travelling waves in hybrid models. Additionally, a numerical comparison between the wave speeds of the continuum models and the hybrid models shows good agreement in the case of weak chemotaxis and qualitative agreement for the strong chemotaxis case. In the case of slow cell adaptation, we detect oscillating behaviour of the wave, which cannot be explained by mean-field approximations.     

Mutagenicity of bi-, tri- and tetra-cyclic aromatic hydrocarbons in the "taped-plate assay" and in the conventional salmonella mutagenicity assay

Aromatic hydrocarbons in the range of 1-4 nuclear rings were examined for mutagenicity in the so-called "taped-plate assay". This modification of the Ames assay is particularly equipped for the detection of volatile mutagens. Of the many compounds tested only phenanthrene, pyrene, benzo[c]phenanthrene and benzoacenaphthylene were positive in this assay. The present data underline the exceptional behaviour of fluoranthene by being a rather potent bacterial mutagen with a volatile nature (as found in a previous study).     

Vigilance Behaviour in White-browed Sparrow-weavers Plocepasser mahali

Group-living white-browed sparrow-weavers engage in vigilance behaviour when fellow group members feed on the ground. Vigilance is characterized from normal perching behaviour by distinct combinations of calls and by exposed perches. The level of vigilance increases with the density of herbacious vegetation. Large groups do not perform less vigilance and more feeding compared with small groups, and are exposed to larger numbers of interactions with predators. This suggests that anti-predator vigilance is an adaptation for surviving high diurnal predation rates, the latter being an effect of the group-living nature of these birds.     

The 1st EMBO workshop on PVC bacteria—Planctomycetes–Verrucomicrobia–Chlamydiae superphylum: Exceptions to the bacterial definition?

The PVC superphylum is a phylogenetically supported collection of various related bacterial phyla that comprise unusual characteristics and traits. The ‘PVC’ abbreviation derives from Planctomycetes, Verrucomicrobia and Chlamydiae as members of this superphylum, while additional bacterial phyla are related. There has recently been increasing and exciting interest in the cell biology, physiology and ecology of members of this superphylum, including evolutionary implications of the complex cell organization of some species. It is timely that international researchers in the PVC superphylum field met to discuss these developments. The first meeting entirely dedicated to those bacteria, the EMBO workshop “PVC superphylum: Exceptions to the bacterial definition” was held at the Heidelberg University to catalyze the formation of a vital scientific community supporting PVC-bacterial research. More than 45 investigators from more than 20 countries (PIs, senior scientists and students) attended the meeting and produced a great starting point for future collaborative research. This Special Issue will focus on the EMBO-PVC meeting. This Perspective briefly summarizes the history of PVC-research, focusing on the key findings and provides a brief summary of the meeting with a focus on the major questions that arose during discussion and that might influence the research in the years to come.     

Universal Response-Adaptation Relation in Bacterial Chemotaxis

The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A short-term memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis.     

Rule-based modelling of conjugative plasmid transfer and incompatibility

COSMIC-rules, an individual-based model for bacterial adaptation and evolution, has been used to study virtual transmission of plasmids within bacterial populations, in an environment varying between supportive and inhibitory. The simulations demonstrate spread of antibiotic resistance (R) plasmids, both compatible and incompatible, by the bacterial gene transfer process of conjugation. This paper describes the behaviour of virtual plasmids, their modes of exchange within bacterial populations and the impact of antibiotics, together with the rules governing plasmid transfer. Three case studies are examined: transfer of an R plasmid within an antibiotic-susceptible population, transfer of two incompatible R plasmids and transfer of two compatible R plasmids. R plasmid transfer confers antibiotic resistance on recipients. For incompatible plasmids, one or other plasmid could be maintained in bacterial cells and only that portion of the population acquiring the appropriate plasmid-encoded resistance survives exposure to the antibiotics. By contrast, the compatible plasmids transfer and mix freely within the bacterial population that survives in its entirety in the presence of the antibiotics. These studies are intended to inform models for examining adaptive evolution in bacteria. They provide proof of principle in simple systems as a platform for predicting the behaviour of bacterial populations in more complex situations, for example in response to changing environments or in multi-species bacterial assemblages.     

Disruptive physiology: olfaction and the microbiome–gut–brain axis

This review covers the field of olfaction and chemosensation of odorants and puts this information into the context of interactions between microbes and behaviour; the microbiome–gut–brain axis (MGBA). Recent emphasis has also been placed on the concept of the holobiome which states that no single aspect of an organism should be viewed separately and thus must include examination of their associated microbial populations and their influence. While it is known that the microbiome may be involved in the modulation of animal behaviour, there has been little systematized effort to incorporate into such studies the rapidly developing knowledge of the wide range of olfactory systems. The classical olfactory system is evolutionarily conserved in multiple taxa from insects through to fish, reptiles and mammals, and is represented by the largest gene families in vertebrates. Mice have over 1000 different olfactory receptors and humans about 400. They are distributed throughout the body and are even found in spermatozoa where they function in chemotaxis. Each olfactory receptor has the unique functional capability of high‐affinity binding to several different molecular ligands. These and other properties render the cataloguing of odorants (odorome) with specific actions a difficult task. Some ectopic olfactory receptors have been shown to have functional effects in the gut and kidney, highlighting the complexity of the systems engaged by odorants. However, there are, in addition to classical olfactory receptors, at least two other families of receptors involved in olfaction that are also widely found expressed on tissues in many different organs in addition to the nervous system and brain: the trace‐amine associated and formyl peptide receptors. Bacteria can make many if not most odorants and are responsible for recognition of species and relative relatedness, as well as predator presence, among many other examples. Activation of different combinations of olfactory receptors by bacterial products such as β‐phenylethylamine have been shown even to control expression of emotions such as fear and aggression. The number of examples of bacterial products and volatile odorants influencing brain function and behaviour is expanding rapidly. Since it is recognized that many different bacterial products and metabolites also function as social cues, and may themselves be directly or indirectly causative of behavioural change, it becomes ever more important to include olfaction into studies of the MGBA. Clearly there are broader implications for the involvement of olfaction in this rapidly evolving field. These include improvement in our understanding of the pathways engaged in various behaviours, and the identification of novel approaches and new targets in efforts to modulate behavioural changes.     

Photoinduced resonance phenomena in the human electroencephalogram as a function of frequency, intensity, and duration of stimulation

The features of resonance phenomena in high-resolution EEG structure were analyzed for two intensities and three values of duration of exposure to 20 constant frequencies of intermittent photic stimulation in a range of 1-20 Hz with 1 Hz steps. It was shown that with a 6 s step duration, an irregular activation of multiple spectral EEG components for both light intensities occurs. With longer durations (12 and 18 s) of fixed-frequency stimulation, the EEG reactions are of resonance nature. Low-intensity flashes cause only the resonance activation of the intrinsic oscillator in the range of dominant alpha-EEG frequency. During a more intensive stimulation, the resonance EEG phenomena are observed for the whole range of stimulation frequencies. The interval of 6-12 s is supposed to be the relaxation period for a system of brain electrical activity generation. After this time, the low-intensity stimuli cause the adaptation of the system to light, whereas more intensive flashes cause more pronounced resonance EEG phenomena and physiological effects.     

Adaptive Remodelling by FliN in the Bacterial Rotary Motor

Sensory adaptation in the Escherichia coli chemosensory pathway has been the subject of interest for decades, with investigation focusing on the receptors that process extracellular inputs. Recent studies demonstrate that the flagellar motors responsible for cell locomotion also play a role, adding or subtracting FliM subunits to maximise sensitivity to pathway signals. It is difficult to reconcile this FliM remodelling with the observation that partner FliN subunits are relatively static fixtures in the motor. By fusing a fluorescent protein internally to FliN, we show that there is in fact significant FliN remodelling. The kinetics and stoichiometry of FliN in steady state and in adapting motors are investigated and found to match the behaviour of FliM in all respects except for timescale where FliN rates are about 4 times slower. We notice that motor adaptation is slower in the presence of the fluorescent protein, indicating a possible source for the difference. The behaviour of FliM and FliN is consistent with a kinetic and stoichiometric model that contradicts the traditional view of a packed, rigid motor architecture.     

Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis I: The Single Cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area.     

Variable sizes of Escherichia coli chemoreceptor signaling teams

Like many sensory receptors, bacterial chemotaxis receptors form clusters. In bacteria, large‐scale clusters are subdivided into signaling teams that act as ‘antennas’ allowing detection of ligands with remarkable sensitivity. The range of sensitivity is greatly extended by adaptation of receptors to changes in concentrations through covalent modification. However, surprisingly little is known about the sizes of receptor signaling teams. Here, we combine measurements of the signaling response, obtained from in vivo fluorescence resonance energy transfer, with the statistical method of principal component analysis, to quantify the size of signaling teams within the framework of the previously successful Monod–Wyman–Changeux model. We find that size of signaling teams increases 2‐ to 3‐fold with receptor modification, indicating an additional, previously unrecognized level of adaptation of the chemotaxis network. This variation of signaling‐team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations.     

HAMP domain structural determinants for signalling and sensory adaptation in Tsr,the Escherichia coli serine chemoreceptor

HAMP domains mediate input–output transactions in many bacterial signalling proteins. To clarify the mechanistic logic of HAMP signalling, we constructed Tsr‐HAMP deletion derivatives and characterized their steady‐state signal outputs and sensory adaptation properties with flagellar rotation and receptor methylation assays. Tsr molecules lacking the entire HAMP domain or just the HAMP‐AS2 helix generated clockwise output signals, confirming that kinase activation is the default output state of the chemoreceptor signalling domain and that attractant stimuli shift HAMP to an overriding kinase‐off signalling state to elicit counter‐clockwise flagellar responses. Receptors with deletions of the AS1 helices, which free the AS2 helices from bundle‐packing constraints, exhibited kinase‐off signalling behaviour that depended on three C‐terminal hydrophobic residues of AS2. We conclude that AS2/AS2′ packing interactions alone can play an important role in controlling output kinase activity. Neither kinase‐on nor kinase‐off HAMP deletion outputs responded to sensory adaptation control, implying that out‐of‐range conformations or bundle‐packing stabilities of their methylation helices prevent substrate recognition by the adaptation enzymes. These observations support the previously proposed biphasic, dynamic‐bundle mechanism of HAMP signalling and additionally show that the structural interplay of helix‐packing interactions between HAMP and the adjoining methylation helices is critical for sensory adaptation control of receptor output.