Modeling and Simulating the Dynamics of Type IV Pili Extension of Pseudomonas aeruginosa

Data-driven modelling makes quantitative predictions regarding bacteria surface motility

In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.

Type IV Pili: Dynamic Bacterial Nanomachines

Bacteria and archaea rely on appendages called type IV pili (T4P) to participate in diverse behaviors including surface sensing, biofilm formation, virulence, protein secretion, and motility across surfaces. T4P are broadly distributed fibers that dynamically extend and retract, and this dynamic activity is essential for their function in broad processes. Despite the essentiality of dynamics in T4P function, little is known about the role of these dynamics and molecular mechanisms controlling them. Recent advances in microscopy have yielded insight into the role of T4P dynamics in their diverse functions and recent structural work has expanded what is known about the inner workings of the T4P motor. This review discusses recent progress in understanding the function, regulation, and mechanisms of T4P dynamics.

Fresh Extension of Vibrio cholerae Competence Type IV Pili Predisposes Them for Motor-Independent Retraction

Bacteria utilize dynamic appendages, called type IV pili (T4P), to interact with their environment and mediate a wide variety of functions. Pilus extension is mediated by an extension ATPase motor, commonly called PilB, in all T4P. Pilus retraction, however, can occur with the aid of an ATPase motor or in the absence of a retraction motor. While much effort has been devoted to studying motor-dependent retraction, the mechanism and regulation of motor-independent retraction remain poorly characterized. We have previously demonstrated that Vibrio cholerae competence T4P undergo motor-independent retraction in the absence of the dedicated retraction ATPases PilT and PilU. Here, we utilize this model system to characterize the factors that influence motor-independent retraction. We find that freshly extended pili frequently undergo motor-independent retraction, but if these pili fail to retract immediately, they remain statically extended on the cell surface. Importantly, we show that these static pili can still undergo motor-dependent retraction via tightly regulated ectopic expression of PilT, suggesting that these T4P are not broken but simply cannot undergo motor-independent retraction. Through additional genetic and biophysical characterization of pili, we suggest that pilus filaments undergo conformational changes during dynamic extension and retraction. We propose that only some conformations, like those adopted by freshly extended pili, are capable of undergoing motor-independent retraction. Together, these data highlight the versatile mechanisms that regulate T4P dynamic activity and provide additional support for the long-standing hypothesis that motor-independent retraction occurs via spontaneous depolymerization. IMPORTANCE Extracellular pilus fibers are critical to the virulence and persistence of many pathogenic bacteria. A crucial function for most pili is the dynamic ability to extend and retract from the cell surface. Inhibiting this dynamic pilus activity represents an attractive approach for therapeutic interventions; however, a detailed mechanistic understanding of this process is currently lacking. Here, we use the competence pilus of Vibrio cholerae to study how pili retract in the absence of dedicated retraction motors. Our results reveal a novel regulatory mechanism of pilus retraction that is an inherent property of the pilus filament. Thus, understanding the conformational changes that pili adopt under different conditions may be critical for the development of novel therapeutics that aim to target the dynamic activity of these structures.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

On the strong connection between nanoscale adhesion of Yad fimbriae and macroscale attachment of Yad-decorated bacteria to glycosylated, hydrophobic and hydrophilic surfaces

Yad fimbriae are currently viewed as versatile bacterial adhesins able to significantly mediate host or plant-pathogen recognition and contribute to the persistence of Escherichia coli in both the environment and within hosts. To date, however, the underlying adhesion process of Yad fimbriae on surfaces defined by controlled coating chemistries has not been evaluated on the relevant molecular scale. In this work, the interaction forces operational between Yad fimbriae expressed by genetically modified E. coli and self-assembled monolayers (SAM) differing in terms of charge, hydrophobicity or the nature of decorating sugar units are quantified by Single Molecule Force Spectroscopy (SMFS) on the nanoscale. It is found that the adhesion of Yad fimbriae onto probes functionalized with xylose is as strong as that measured with probes decorated with anti-Yad antibodies (ca. 80 to 300 pN). In contrast, the interactions of Yad with galactose, lactose, mannose, -OH, -NH₂, -COOH and -CH₃ terminated SAMs are clearly non-specific. Interpretation of SMFS measurements on the basis of worm-like-chain modeling for polypeptide nanomechanics further leads to the estimates of the maximal extension of Yad fimbriae upon stretching, of their persistence length and of their polydispersity. Finally, we show for the first time a strong correlation between the adhesion properties of Yad-decorated bacteria determined from conventional macroscopic counting methods and the molecular adhesion capacity of Yad fimbriae. This demonstration advocates the effort that should be made to understand on the nanoscale level the interactions between fimbriae and their cognate ligands. The results could further help the design of potential anti-adhesive molecules or surfaces to better fight against the virulence of bacterial pathogens.

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. In particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. Twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities.

Modelling bacterial twitching in fluid flows: a CFD-DEM approach

Bacterial habitats are often associated with fluid flow environments. Bacterial twitching is important for initial bacterial colonization and biofilm formation. The existing research about bacteria twitching is largely experimental orientated. There is a lack of models of twitching motility of bacteria in shear flows, which could provide fundamental understanding about how bacterial twitching would be affected by bacteria associated properties such as number of pili and their distribution on the cell body and environmental factors such as flow and surface patterns. In this work, a three-dimensional modelling approach of Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM) proposed to study bacterial twitching on flat and groove surfaces under shear flow conditions. Rod-shaped bacteria are modelled as groups of spherical particles and Type IV pili attached to bacteria are modelled as dynamic springs which can elongate, retract, attach and detach. The CFD-DEM model of rod-shape bacteria is validated against orbiting of immotile bacteria in shear flows. The effects of fluid flow rate and surface topography on twitching motility are studied. The model can successfully predict upstream twitching motility of rod-shaped bacteria in shear flows. Our model can predict that there would be an optimal range of wall shear stress in which bacterial upstream twitching is most efficient. The results also indicate that when bacteria twitch on groove surfaces, they are likely to accumulate around the downstream side of the groove walls.

How bacterial cells and colonies move on solid substrates

Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple pili. It was shown experimentally that the substrate motility of Neisseria gonorrhoeae cells can be described as a persistent random walk with a persistence length that exceeds the mean pili length. Moreover, the persistence length increases for a higher number of pili per cell. With the help of a simple, tractable stochastic model, we test whether a tug of war without directional memory can explain the persistent motion of single Neisseria gonorrhoeae cells. While persistent motion of single cells indeed emerges naturally in the model, a tug of war alone is not capable of explaining the motility of microcolonies, which becomes weaker with increasing colony size. We suggest sliding friction between the microcolonies and the substrate as the missing ingredient. While such friction almost does not affect the general mechanism of single cell motility, it has a strong effect on colony motility. We validate the theoretical predictions by using a three-dimensional computational model that includes explicit details of the pili dynamics, force generation, and geometry of cells.

The Dynamic Structures of the Type IV Pilus

Type IV pilus (T4P)-like systems have been identified in almost every major phylum of prokaryotic life. They include the type IVa pilus (T4aP), type II secretion system (T2SS), type IVb pilus (T4bP), Tad/Flp pilus, Com pilus, and archaeal flagellum (archaellum). These systems are used for adhesion, natural competence, phage adsorption, folded-protein secretion, surface sensing, swimming motility, and twitching motility. The T4aP allows for all of these functions except swimming and is therefore a good model system for understanding T4P-like systems. Recent structural analyses have revolutionized our understanding of how the T4aP machinery assembles and functions. Here we review the structure and function of the T4aP.