Dynamic motors for bacterial flagella

Silver Ions Inhibit Bacterial Movement and Stall Flagellar Motor

Silver (Ag) in different forms has been gaining broad attention due to its antimicrobial activities and the increasing resistance of bacteria to commonly prescribed antibiotics. However, various aspects of the antimicrobial mechanism of Ag have not been understood, including how Ag affects bacterial motility, a factor intimately related to bacterial virulence. Here, we report our study on how Ag⁺ ions affect the motility of E. coli bacteria using swimming, tethering, and rotation assays. We observed that the bacteria slowed down dramatically by >70% when subjected to Ag⁺ ions, providing direct evidence that Ag⁺ ions inhibit the motility of bacteria. In addition, through tethering and rotation assays, we monitored the rotation of flagellar motors and observed that the tumbling/pausing frequency of bacteria increased significantly by 77% in the presence of Ag⁺ ions. Furthermore, we analyzed the results from the tethering assay using the hidden Markov model (HMM) and found that Ag⁺ ions decreased bacterial tumbling/pausing-to-running transition rate significantly by 75%. The results suggest that the rotation of bacterial flagellar motors was stalled by Ag⁺ ions. This work provided a new quantitative understanding of the mechanism of Ag-based antimicrobial agents in bacterial motility.

Shining light in blind alleys: deciphering bacterial attachment in silicon microstructures

With new advances in infectious disease, antifouling surfaces, and environmental microbiology research comes the need to understand and control the accumulation and attachment of bacterial cells on a surface. Thus, we employ intrinsic phase-shift reflectometric interference spectroscopic measurements of silicon diffraction gratings to non-destructively observe the interactions between bacterial cells and abiotic, microstructured surfaces in a label-free and real-time manner. We conclude that the combination of specific material characteristics (i.e., substrate surface charge and topology) and characteristics of the bacterial cells (i.e., motility, cell charge, biofilm formation, and physiology) drive bacteria to adhere to a particular surface, often leading to a biofilm formation. Such knowledge can be exploited to predict antibiotic efficacy and biofilm formation, and enhance surface-based biosensor development, as well as the design of anti-biofouling strategies.

Implication of Surface Properties, Bacterial Motility, and Hydrodynamic Conditions on Bacterial Surface Sensing and Their Initial Adhesion

Biofilms are structured microbial communities attached to surfaces, which play a significant role in the persistence of biofoulings in both medical and industrial settings. Bacteria in biofilms are mostly embedded in a complex matrix comprised of extracellular polymeric substances that provide mechanical stability and protection against environmental adversities. Once the biofilm is matured, it becomes extremely difficult to kill bacteria or mechanically remove biofilms from solid surfaces. Therefore, interrupting the bacterial surface sensing mechanism and subsequent initial binding process of bacteria to surfaces is essential to effectively prevent biofilm-associated problems. Noting that the process of bacterial adhesion is influenced by many factors, including material surface properties, this review summarizes recent works dedicated to understanding the influences of surface charge, surface wettability, roughness, topography, stiffness, and combination of properties on bacterial adhesion. This review also highlights other factors that are often neglected in bacterial adhesion studies such as bacterial motility and the effect of hydrodynamic flow. Lastly, the present review features recent innovations in nanotechnology-based antifouling systems to engineer new concepts of antibiofilm surfaces.

How microbes read the map: Effects of implant topography on bacterial adhesion and biofilm formation

Microbes have remarkable capabilities to attach to the surface of implanted medical devices and form biofilms that adversely impact device function and increase the risk of multidrug-resistant infections. The physicochemical properties of biomaterials have long been known to play an important role in biofilm formation. More recently, a series of discoveries in the natural world have stimulated great interest in the use of 3D surface topography to engineer antifouling materials that resist bacterial colonization. There is also increasing evidence that some medical device surface topographies, such as those designed for tissue integration, may unintentionally promote microbial attachment. Despite a number of reviews on surface topography and biofilm control, there is a missing link between how bacteria sense and respond to 3D surface topographies and the rational design of antifouling materials. Motivated by this gap, we present a review of how bacteria interact with surface topographies, and what can be learned from current laboratory studies of microbial adhesion and biofilm formation on specific topographic features and medical devices. We also address specific biocompatibility considerations and discuss how to improve the assessment of the anti-biofilm performance of topographic surfaces. We conclude that 3D surface topography, whether intended or unintended, is an important consideration in the rational design of safe medical devices. Future research on next-generation smart antifouling materials could benefit from a greater focus on translation to real-world applications.

Reversible Interconversion of a Static Metallosupramolecular Cage Assembly into a High-Speed Rotor: Stepless Adjustment of Rotational Exchange by Nucleophile Addition

The self-assembled cage ROT-1 was prepared from the pyridine-terminated rotator 1, the phenanthroline-appended stator 2, DABCO, and copper(I) ions in a ratio of 1:1:1:4. This four-component assembly is held together by two pyridine→[Cu(phenAr₂)]⁺ as well as two DABCO→zinc porphyrin interactions (phenAr₂ = 2,9-diarylphenanthroline) and does not show any motion on the NMR time scale ( k < 0.1 s^-1, 298 K). However, it is converted to the fast nanorotor ROT-1 _x^CD₃CN by addition of CD₃CN [ x = (v/v)% of acetonitrile in dichloromethane] due to acceleration of both pyridine→copper(I) dissociation steps. Now the rotator is able to visit all four copper(I)-loaded phenanthroline stations of the stator. Depending on the amount of CD₃CN, the exchange frequency of the nanorotor varies from 0.7 s^-1 (CD₃CN:CD₂Cl₂ = 1:29) to 8000 s^-1 (CD₃CN:CD₂Cl₂ = 1:5) at 25 °C. When iodide (I^-) is added to the static assembly ROT-1, the rotational speed increases even more drastically ( k = 20 000 s^-1), again due to accelerating the rate-determining pyridine→copper(I) dissociation step. In both cases, a sigmoidal relationship is established between exchange frequency and the concentration of added nucleophile (CD₃CN or iodide) that suggests the presence of a cooperative effect. Reversible switching between the static assembly and fast rotor was performed several times without any decomposition of the system. In contrast, addition of the common nucleophile PPh₃ to ROT-1 does not increase the rotational speed, a finding that is explained on thermodynamic grounds.

Reconstructing the genotype-to-fitness map for the bacterial chemotaxis network and its emergent behavioural phenotypes

The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes. Mutant genotypes differ from the wildtype in the concentrations of one or more constituent proteins of the chemotaxis signalling network or in one or more of its kinetic parameters. To guarantee model consistency across the genotype space, we explicitly incorporated biochemical constraints that underly observed phenotypic trade-offs. The model was validated by reconstructing the phenotypic properties of several known mutant genotypes. We also characterised differences in the fitness distribution between genotypes, and reconstructed adaptive walks in genotype space for populations exposed to different environmental conditions. We found that the local fitness landscape is rugged, due to non-additive interactions between mutations. When selection has a consistent direction, just a few adaptive mutations are required to reach a local peak, and different local peaks can be reached by adaptive walks starting from the same initial genotype. However, when the direction of selection is fluctuating, evolutionary paths are much longer and genotype space is explored further. Longer adaptive walks were also observed when evolution was started from a low-fitness genotype such as a CheZ knockout mutant. In line with empirical observations, the initial ΔcheZ mutant did not respond to a step-down stimulus, but a dynamic response similar to the wildtype was recovered following the fixation of compensatory mutations.

Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum

Rhodospirillum rubrum possesses a novel oxygen-independent, aerobic methionine salvage pathway (MSP) for recycling methionine from 5-methylthioadenosine (MTA), the MTA-isoprenoid shunt. This organism can also metabolize MTA as a sulfur source under anaerobic conditions, suggesting that the MTA-isoprenoid shunt may also function anaerobically as well. In this study, deep proteomics profiling, directed metabolite analysis, and reverse transcriptase quantitative PCR (RT-qPCR) revealed metabolic changes in response to anaerobic growth on MTA versus sulfate as sole sulfur source. The abundance of protein levels associated with methionine transport, cell motility, and chemotaxis increased in the presence of MTA over that in the presence of sulfate. Purine salvage from MTA resulted primarily in hypoxanthine accumulation and a decrease in protein levels involved in GMP-to-AMP conversion to balance purine pools. Acyl coenzyme A (acyl-CoA) metabolic protein levels for lipid metabolism were lower in abundance, whereas poly-β-hydroxybutyrate synthesis and storage were increased nearly 10-fold. The known R. rubrum aerobic MSP was also shown to be upregulated, to function anaerobically, and to recycle MTA. This suggested that other organisms with gene homologues for the MTA-isoprenoid shunt may also possess a functioning anaerobic MSP. In support of our previous findings that ribulose-1,5-carboxylase/oxygenase (RubisCO) is required for an apparently purely anaerobic MSP, RubisCO transcript and protein levels both increased in abundance by over 10-fold in cells grown anaerobically on MTA over those in cells grown on sulfate, resulting in increased intracellular RubisCO activity. These results reveal for the first time global metabolic responses as a consequence of anaerobic MTA metabolism compared to using sulfate as the sulfur source.

In nearly all organisms, sulfur-containing byproducts result from many metabolic reactions. Unless these compounds are further metabolized, valuable organic sulfur is lost and can become limiting. To regenerate the sulfur-containing amino acid methionine, organisms typically employ one of several variations of a “universal” methionine salvage pathway (MSP). A common aspect of the universal MSP is a final oxygenation step. This work establishes that the metabolically versatile bacterium Rhodospirillum rubrum employs a novel MSP that does not require oxygen under either aerobic or anaerobic conditions. There is also a separate, dedicated anaerobic MTA metabolic route in R. rubrum. This work reveals global changes in cellular metabolism in response to anaerobic MTA metabolism compared to using sulfate as a sulfur source. We found that cell mobility and transport were enhanced, along with lipid, nucleotide, and carbohydrate metabolism, when cells were grown in the presence of MTA.

Bio-Hybrid Micro/Nanodevices Powered by Flagellar Motor: Challenges and Strategies

Molecular motors, which are precision engineered by nature, offer exciting possibilities for bio-hybrid engineered systems. They could enable real applications ranging from micro/nano fluidics, to biosensing, to medical diagnoses. This review describes the fundamental biological insights and fascinating potentials of these remarkable sensing and actuation machines, in particular, bacterial flagellar motors, as well as their engineering perspectives with regard to applications in bio-engineered hybrid systems.

Essential validation methods for E. coli strains created by chromosome engineering

BACKGROUND

Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, λ-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain's chromosome.

RESULTS AND DISCUSSION

Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check.

CONCLUSION

The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.

Mechanism for adaptive remodeling of the bacterial flagellar switch

The bacterial flagellar motor has been shown in previous work to adapt to changes in the steady-state concentration of the chemotaxis signaling molecule, CheY-P, by changing the FliM content. We show here that the number of FliM molecules in the motor and the fraction of FliM molecules that exchange depend on the direction of flagellar rotation, not on CheY-P binding per se. Our results are consistent with a model in which the structural differences associated with the direction of rotation modulate the strength of FliM binding. When the motor spins counterclockwise, FliM binding strengthens, the fraction of FliM molecules that exchanges decreases, and the ring content increases. The larger number of CheY-P binding sites enhances the motor's sensitivity, i.e., the motor adapts. An interesting unresolved question is how additional copies of FliM might be accommodated.

Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria

Flagellar and translocation-associated type III secretion (T3S) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.

Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging

Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry.