Information processing in bacterial chemotaxis

I like therefore I can, and I can therefore I like: the role of self-efficacy and affect in active inference of allostasis

Active inference (AIF) is a theory of the behavior of information-processing open dynamic systems. It describes them as generative models (GM) generating inferences on the causes of sensory input they receive from their environment. Based on these inferences, GMs generate predictions about sensory input. The discrepancy between a prediction and the actual input results in prediction error. GMs then execute action policies predicted to minimize the prediction error. The free-energy principle provides a rationale for AIF by stipulating that information-processing open systems must constantly minimize their free energy (through suppressing the cumulative prediction error) to avoid decay. The theory of homeostasis and allostasis has a similar logic. Homeostatic set points are expectations of living organisms. Discrepancies between set points and actual states generate stress. For optimal functioning, organisms avoid stress by preserving homeostasis. Theories of AIF and homeostasis have recently converged, with AIF providing a formal account for homeo- and allostasis. In this paper, we present bacterial chemotaxis as molecular AIF, where mutual constraints by extero- and interoception play an essential role in controlling bacterial behavior supporting homeostasis. Extending this insight to the brain, we propose a conceptual model of the brain homeostatic GM, in which we suggest partition of the brain GM into cognitive and physiological homeostatic GMs. We outline their mutual regulation as well as their integration based on the free-energy principle. From this analysis, affect and self-efficacy emerge as the main regulators of the cognitive homeostatic GM. We suggest fatigue and depression as target neurocognitive phenomena for studying the neural mechanisms of such regulation.

Towards the Idea of Molecular Brains

How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

Background

Many bacteria and certain eukaryotes utilize multi-step His-to-Asp phosphorelays for adaptive responses to their extracellular environments. Histidine phosphotransfer (HPt) proteins function as key components of these pathways. HPt proteins are genetically diverse, but share a common tertiary fold with conserved residues near the active site. A surface-exposed glycine at the H + 4 position relative to the phosphorylatable histidine is found in a significant number of annotated HPt protein sequences. Previous reports demonstrated that substitutions at this position result in diminished phosphotransfer activity between HPt proteins and their cognate signaling partners.

Results

We report the analysis of partner binding interactions and phosphotransfer activity of the prototypical HPt protein Ypd1 from Saccharomyces cerevisiae using a set of H + 4 (G68) substituted proteins. Substitutions at this position with large, hydrophobic, or charged amino acids nearly abolished phospho-acceptance from the receiver domain of its upstream signaling partner, Sln1 (Sln1-R1). An in vitro binding assay indicated that G68 substitutions caused only modest decreases in affinity between Ypd1 and Sln1-R1, and these differences did not appear to be large enough to account for the observed decrease in phosphotransfer activity. The crystal structure of one of these H + 4 mutants, Ypd1-G68Q, which exhibited a diminished ability to participate in phosphotransfer, shows a similar overall structure to that of wild-type. Molecular modelling suggests that the highly conserved active site residues within the receiver domain of Sln1 must undergo rearrangement to accommodate larger H + 4 substitutions in Ypd1.

Conclusions

Phosphotransfer reactions require precise arrangement of active site elements to align the donor-acceptor atoms and stabilize the transition state during the reaction. Any changes likely result in an inability to form a viable transition state during phosphotransfer. Our data suggest that the high degree of evolutionary conservation of residues with small side chains at the H + 4 position in HPt proteins is required for optimal activity and that the presence of larger residues at the H + 4 position would cause alterations in the positioning of active site residues in the partner response regulator.

Electronic supplementary material

The online version of this article (10.1186/s12858-019-0104-5) contains supplementary material, which is available to authorized users.

Functional Membrane Microdomains Organize Signaling Networks in Bacteria

Membrane organization is usually associated with the correct function of a number of cellular processes in eukaryotic cells as diverse as signal transduction, protein sorting, membrane trafficking, or pathogen invasion. It has been recently discovered that bacterial membranes are able to compartmentalize their signal transduction pathways in functional membrane microdomains (FMMs). In this review article, we discuss the biological significance of the existence of FMMs in bacteria and comment on possible beneficial roles that FMMs play on the harbored signal transduction cascades. Moreover, four different membrane-associated signal transduction cascades whose functions are linked to the integrity of FMMs are introduced, and the specific role that FMMs play in stabilizing and promoting interactions of their signaling components is discussed. Altogether, FMMs seem to play a relevant role in promoting more efficient activation of signal transduction cascades in bacterial cells and show that bacteria are more sophisticated organisms than previously appreciated.

Elements of the cellular metabolic structure

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.

The cognitive cell: bacterial behavior reconsidered

Research on how bacteria adapt to changing environments underlies the contemporary biological understanding of signal transduction (ST), and ST provides the foundation of the information-processing approach that is the hallmark of the ‘cognitive revolution,’ which began in the mid-20th century. Yet cognitive scientists largely remain oblivious to research into microbial behavior that might provide insights into problems in their own domains, while microbiologists seem equally unaware of the potential importance of their work to understanding cognitive capacities in multicellular organisms, including vertebrates. Evidence in bacteria for capacities encompassed by the concept of cognition is reviewed. Parallels exist not only at the heuristic level of functional analogue, but also at the level of molecular mechanism, evolution and ecology, which is where fruitful cross-fertilization among disciplines might be found.

Expression level of a chimeric kinase governs entry into sporulation in Bacillus subtilis

Upon starvation, Bacillus subtilis cells switch from growth to sporulation. It is believed that the N-terminal sensor domain of the cytoplasmic histidine kinase KinA is responsible for detection of the sporulation-specific signal(s) that appears to be produced only under starvation conditions. Following the sensing of the signal, KinA triggers autophosphorylation of the catalytic histidine residue in the C-terminal domain to transmit the phosphate moiety, via phosphorelay, to the master regulator for sporulation, Spo0A. However, there is no direct evidence to support the function of the sensor domain, because the specific signal(s) has never been found. To investigate the role of the N-terminal sensor domain, we replaced the endogenous three-PAS repeat in the N-terminal domain of KinA with a two-PAS repeat derived from Escherichia coli and examined the function of the resulting chimeric protein. Despite the introduction of a foreign domain, we found that the resulting chimeric protein, in a concentration-dependent manner, triggered sporulation by activating Spo0A through phosphorelay, irrespective of nutrient availability. Further, by using chemical cross-linking, we showed that the chimeric protein exists predominantly as a tetramer, mediated by the N-terminal domain, as was found for KinA. These results suggest that tetramer formation mediated by the N-terminal domain, regardless of the origin of the protein, is important and sufficient for the kinase activity catalyzed by the C-terminal domain. Taken together with our previous observations, we propose that the primary role of the N-terminal domain of KinA is to form a functional tetramer, but not for sensing an unknown signal.

Thermal domain motions of CheA kinase in solution: Disulfide trapping reveals the motional constraints leading to trans-autophosphorylation

The histidine kinase CheA is a central component of the bacterial chemotaxis signaling cluster, in which transmembrane receptors regulate CheA autokinase activity. CheA is a homodimer, and each of the two identical subunits possesses five different domains with distinct structures and functions. The free enzyme, like the receptor-bound enzyme, catalyzes a trans-autokinase reaction in which the catalytic domain (P4) of one subunit phosphorylates the substrate domain (P1) of the other subunit. Molecular analysis of CheA domain motions has important implications for the mechanism of CheA trans-autophosphorylation, for CheA assembly into the signaling cluster and for receptor regulation of CheA activity. In this initial study of the free CheA dimer, we employ disulfide trapping to analyze collisions between pairs of domains, thereby mapping out the ranges and kinetics of domain motions. A library of 33 functional single-cysteine CheA mutants, all retaining normal autokinase activity, is used to analyze intradimer collisions between symmetric domain pairs. The homodimeric structure of CheA ensures that each mutant contains a pair of symmetric, surface-exposed cysteine residues. Cysteine-cysteine collisions trapped by disulfide bond formation indicate that P1 is the most mobile CheA domain, but large amplitude P2, P4, and P5 domain motions are also detected. The mobility of P1 is further analyzed using a library of 17 functional dicysteine CheA mutants, wherein each mutant subunit possesses one cysteine at a fixed probe position on the P1 domain and a second cysteine on a different domain. The resulting CheA homodimers contain four cysteine residues; thus disulfide trapping yields multiple products that are identified by assignment methods. The findings reveal that the P1 substrate domain collides rapidly with residues on the P4' catalytic domain in the sister subunit, but no intrasubunit collisions are detected. This observation provides a direct, motional explanation for CheA trans-autophosphorylation, explains why the long linkers of the P1-P2 region do not become tangled in the dimer, and has important implications for other aspects of CheA function. Finally, a working model is proposed for the motional constraints that limit the P1 domain to the region of space near the P4' catalytic domain of the sister subunit.

Individuality in bacteria

While traditionally microbiologists have examined bacterial behavior averaged over large populations, increasingly we are becoming aware that bacterial populations can be composed of phenotypically diverse individuals generated by a variety of mechanisms. Though the results of different mechanisms, the phenomena of bistability, persistence, variation in chemotactic response, and phase and antigenic variation are all strategies to develop population-level diversity. The understanding of individuality in bacteria requires an appreciation of their environmental and ecological context, and thus evolutionary theory regarding adaptations to time-variable environments is becoming more applicable to these problems. In particular, the application of game and information theory to bacterial individuality has addressed some interesting problems of bacterial behavior. In this review we discuss the mechanisms of generating population-level variability, and the application of evolutionary theory to problems of individuality in bacteria.

The diverse CheC-type phosphatases: chemotaxis and beyond

A new class of protein phosphatases has emerged in the study of bacterial/archaeal chemotaxis, the CheC-type phosphatases. These proteins are distinct and unrelated to the well-known CheY-P phosphatase CheZ, though they have convergently evolved to dephosphorylate the same target. The family contains a common consensus sequence D/S-X(3)-E-X(2)-N-X(22)-P that defines the phosphatase active site, of which there are often two per protein. Three distinct subgroups make up the family: CheC, FliY and CheX. Further, the CheC subgroup can be divided into three classes. Bacillus subtilis CheC typifies the first class and might function as a regulator of CheD. Class II CheCs likely function as phosphatases in systems other than chemotaxis. Class III CheCs are found in the archaeal class Halobacteria and might function as class I CheCs. FliY is the main phosphatase in the B. subtilis chemotaxis system. CheX is quite divergent from the rest of the family, forms a dimer and some may function outside chemotaxis. A model for the evolution of the family is discussed.

Stimulus perception in bacterial signal-transducing histidine kinases

Two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. They consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. Histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. They can be identified and classified by virtue of their conserved cytoplasmic kinase domains. In contrast, the sensor domains are highly variable, reflecting the plethora of different signals and modes of sensing. In order to gain insight into the mechanisms of stimulus perception by bacterial histidine kinases, we here survey sensor domain architecture and topology within the bacterial membrane, functional aspects related to this topology, and sequence and phylogenetic conservation. Based on these criteria, three groups of histidine kinases can be differentiated. (i) Periplasmic-sensing histidine kinases detect their stimuli (often small solutes) through an extracellular input domain. (ii) Histidine kinases with sensing mechanisms linked to the transmembrane regions detect stimuli (usually membrane-associated stimuli, such as ionic strength, osmolarity, turgor, or functional state of the cell envelope) via their membrane-spanning segments and sometimes via additional short extracellular loops. (iii) Cytoplasmic-sensing histidine kinases (either membrane anchored or soluble) detect cellular or diffusible signals reporting the metabolic or developmental state of the cell. This review provides an overview of mechanisms of stimulus perception for members of all three groups of bacterial signal-transducing histidine kinases.

Simulating the evolution of signal transduction pathways

We use a generic model of a network of proteins that can activate or deactivate each other to explore the emergence and evolution of signal transduction networks and to gain a basic understanding of their general properties. Starting with a set of non-interacting proteins, we evolve a signal transduction network by random mutation and selection to fulfill a complex biological task. In order to validate this approach we base selection on a fitness function that captures the essential features of chemotactic behavior as seen in bacteria. We find that a system of as few as three proteins can evolve into a network mediating chemotaxis-like behavior by acting as a "derivative sensor". Furthermore, we find that the dynamics and topology of such networks show many similarities to the natural chemotaxis pathway, that the response magnitude can increase with increasing network size and that network behavior shows robustness towards variations in some of the internal parameters. We conclude that simulating the evolution of signal transduction networks to mediate a certain behavior may be a promising approach for understanding the general properties of the natural pathway for that behavior.

Signal transduction networks: topology, response and biochemical processes

Conventionally, biological signal transduction networks are analysed using experimental and theoretical methods to describe specific protein components, interactions, and biochemical processes and to model network behavior under various conditions. While these studies provide crucial information on specific networks, this information is not easily converted to a broader understanding of signal transduction systems. Here, using a specific model of protein interaction we analyse small network topologies to understand their response and general properties. In particular, we catalogue the response for all possible topologies of a given network size to generate a response distribution, analyse the effects of specific biochemical processes on this distribution, and analyse the robustness and diversity of responses with respect to internal fluctuations or mutations in the network. The results show that even three- and four-protein networks are capable of creating diverse and biologically relevant responses, that the distribution of response types changes drastically as a function of biochemical processes at protein level, and that certain topologies strongly pre-dispose a specific response type while others allow for diverse types of responses. This study sheds light on the response types and properties that could be expected from signal transduction networks, provides possible explanations for the role of certain biochemical processes in signal transduction and suggests novel approaches to interfere with signaling pathways at the molecular level. Furthermore it shows that network topology plays a key role on determining response type and properties and that proper representation of network topology is crucial to discover and understand so-called building blocks of large networks.

Time-resolved detection of sensory rhodopsin II-transducer interaction

The dynamics of protein conformational change of Natronobacterium pharaonis sensory rhodopsin II (NpSRII) and of NpSRII fused to cognate transducer (NpHtrII) truncated at 159 amino acid sequence from the N-terminus (NpSRII-DeltaNpHtrII) are investigated in solution phase at room temperature by the laser flash photolysis and the transient grating methods in real time. The diffusion coefficients of both species indicate that the NpSRII-DeltaNpHtrII exists in the dimeric form in 0.6% dodecyl-beta-maltopyranoside (DM) solution. Rate constants of the reaction processes in the photocycles determined by the transient absorption and grating methods agree quite well. Significant differences were found in the volume change and the molecular energy between NpSRII and NpSRII-DeltaNpHtrII samples. The enthalpy of the second intermediate (L) of NpSRII-DeltaNpHtrII is more stabilized compared with that of NpSRII. This stabilization indicates the influence of the transducer to the NpSRII structure in the early intermediate species by the complex formation. Relatively large molecular volume expansion and contraction were observed in the last two steps for NpSRII. Additional volume expansion and contraction were induced by the presence of DeltaNpHtrII. This volume change, which should reflect the conformational change induced by the transducer protein, suggested that this is the signal transduction process of the NpSRII-DeltaNpHtrII.

Three-dimensional electron microscopic imaging of membrane invaginations in Escherichia coli overproducing the chemotaxis receptor Tsr

Electron tomography is a powerful method for determining the three-dimensional structures of large macromolecular assemblies, such as cells, organelles, and multiprotein complexes, when crystallographic averaging methods are not applicable. Here we used electron tomographic imaging to determine the molecular architecture of Escherichia coli cells engineered to overproduce the bacterial chemotaxis receptor Tsr. Tomograms constructed from fixed, cryosectioned cells revealed that overproduction of Tsr led to formation of an extended internal membrane network composed of stacks and extended tubular structures. We present an interpretation of the tomogram in terms of the packing arrangement of Tsr using constraints derived from previous X-ray and electron-crystallographic studies of receptor clusters. Our results imply that the interaction between the cytoplasmic ends of Tsr is likely to stabilize the presence of the membrane networks in cells overproducing Tsr. We propose that membrane invaginations that are potentially capable of supporting axial interactions between receptor clusters in apposing membranes could also be present in wild-type E. coli and that such receptor aggregates could play an important role in signal transduction during bacterial chemotaxis.

Diversity in chemotaxis mechanisms among the bacteria and archaea

The study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. In bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. Most insights into the processes involved have come from studies of Escherichia coli over the last three decades. However, in the last 10 years, with the sequencing of many prokaryotic genomes, it has become clear that E. coli represents a streamlined example of bacterial chemotaxis. While general features of excitation remain conserved among bacteria and archaea, specific features, such as adaptational processes and hydrolysis of the intracellular signal CheY-P, are quite diverse. The Bacillus subtilis chemotaxis system is considerably more complex and appears to be similar to the one that existed when the bacteria and archaea separated during evolution, so that understanding this mechanism should provide insight into the variety of mechanisms used today by the broad sweep of chemotactic bacteria and archaea. However, processes even beyond those used in E. coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli.

Swarming populations of Salmonella represent a unique physiological state coupled to multiple mechanisms of antibiotic resistance

Salmonella enterica serovar Typhimurium is capable of swarming over semi-solid surfaces. Although its swarming behavior shares many readily observable similarities with other swarming bacteria, the phenomenon remains somewhat of an enigma in this bacterium since some attributes skew away from the better characterized systems. Swarming is quite distinct from the classic swimming motility, as there is a prerequisite for cells to first undergo a morphological transformation into swarmer cells. In some organisms, swarming is controlled by quorum sensing, and in others, swarming has been shown to be coupled to increased expression of important virulence factors. Swarming in serovar Typhimurium is coupled to elevated resistance to a wide variety of structurally and functionally distinct classes of antimicrobial compounds. As serovar Typhimurium differentiates into swarm cells, the pmrHFIJKLM operon is up-regulated, resulting in a more positively charged LPS core. Furthermore, as swarm cells begin to de-differentiate, the pmr operon expression is down-regulated, rapidly reaching the levels observed in swim cells. This is one potential mechanism which confers swarm cells increased resistance to antibiotics such as the cationic antimicrobial peptides. However, additional mechanisms are likely associated with the cells in the swarm state that confer elevated resistance to such a broad spectrum of antimicrobial agents.

The BglF sensor recruits the BglG transcription regulator to the membrane and releases it on stimulation

The Escherichia coli BglF protein is a sugar-sensor that controls the activity of the transcriptional antiterminator BglG by reversibly phosphorylating it, depending on beta-glucoside availability. BglF is a membrane-bound protein, whereas BglG is a soluble protein, and they are both present in the cell in minute amounts. How do BglF and BglG find each other to initiate signal transduction efficiently? Using bacterial two-hybrid systems and the Far-Western technique, we demonstrated unequivocally that BglG binds to BglF and to its active site-containing domain in vivo and in vitro. Measurements by surface plasmon resonance corroborated that the affinity between these proteins is high enough to enable their stable binding. To visualize the subcellular localization of BglG, we used fluorescence microscopy. In cells lacking BglF, the BglG-GFP fusion protein was evenly distributed throughout the cytoplasm. In contrast, in cells producing BglF, BglG-GFP was localized to the membrane. On addition of beta-glucoside, BglG-GFP was released from the membrane, becoming evenly distributed throughout the cell. Using mutant proteins and genetic backgrounds that impede phosphorylation of the Bgl proteins, we demonstrated that BglG-BglF binding and recruitment of BglG to the membrane sensor requires phosphorylation but does not depend on the individual phosphorylation sites of the Bgl proteins. We suggest a mechanism for rapid response to environmental changes by preassembly of signaling complexes, which contain transcription regulators recruited by their cognate sensors-kinases, under nonstimulating conditions, and release of the regulators to the cytoplasm on stimulation. This mechanism might be applicable to signaling cascades in prokaryotes and eukaryotes.

Swarm-cell differentiation in Salmonella enterica serovar typhimurium results in elevated resistance to multiple antibiotics

Although a wealth of knowledge exists about the molecular and biochemical mechanisms governing the swimming motility of Salmonella enterica serovar Typhimurium, its surface swarming behavior has not been extensively characterized. When inoculated onto a semisolid agar medium supplemented with appropriate nutrients, serovar Typhimurium undergoes a morphological differentiation whereby single cells hyperflagellate and elongate into nonseptate, multinucleate swarm cells. Swarm migration is a collective behavior of groups of cells. We have isolated a MudJ insertion mutant of serovar Typhimurium 14028 that failed to swarm under any conditions. The site of the MudJ insertion was determined to be in the pmrK locus within the pmrHFIJKLM operon, which was previously demonstrated to confer resistance to cationic antimicrobial peptides. beta-Galactosidase assays, using the pmrK::lacZ transcriptional fusion, showed increased expression of the pmr operon in swarm cells compared to that in vegetative cells. In concurrence with the expression data, swarm cells exhibited greater tolerance to polymyxin. To compare the profiles of vegetative and swarm-cell resistance to other antibiotics, E-test strips representing a wide range of antibiotic classes were used. Swarm cells exhibited elevated resistance to a variety of antibiotics, including those that target the cell envelope, protein translation, DNA replication, and transcription. These observations, in addition to the dramatic morphological changes associated with the swarming phenotype, provide an intriguing model for examining global differences between the physiological states of vegetative and swarm cells of serovar Typhimurium.