The younger flagellum sets the beat for Chlamydomonas reinhardtii.

Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates' tactic behaviors.

Many single-cell organisms use tiny hair-like structures called flagella to move around. To direct this movement, the flagella must work together and beat in a synchronous manner. In some organisms, coordination is achieved by each flagellum reacting to the flow generated by neighbouring flagella. In others, flagella are joined together by fiber connections between their bases, which allow movement to be coordinated through mechanical signals sent between flagella. One such organism is Chlamydomonas reinhardtii, a type of algae frequently used to study flagellar coordination. Its two flagella ­ named trans and cis because of their positions relative to the cell's eyespot ­ propel the cell through water using breaststroke-like movements. To steer, C. reinhardtii adjusts the strength of the strokes made by each flagellum. Despite this asymmetry, the flagella must continue to beat in synchrony to move efficiently. To understand how the cell manages these differences, Wei et al. exposed each flagellum to carefully generated oscillations in water so that each was exposed to different forces and their separate responses could be measured. A combination of experiments, modelling and computer simulations were then used to work out how the two flagella coordinate to steer the cell. Wei et al. found that only the cis flagellum coordinates the beating, with the trans flagellum simply copying the motion of the cis. A direct consequence of such one-way coupling is that only forces on the cis flagellum influence the coordinated beating dynamics of both flagella. These findings shed light on the unique roles of each flagellum in the coordinated movement in C. reinhardtii and have implications for how other organisms with mechanically-connected flagella navigate their environments.

Growth, Distribution, and Photosynthesis of Chlamydomonas Reinhardtii in 3D Hydrogels.

Engineered living materials (ELMs) are a novel class of functional materials that typically feature spatial confinement of living components within an inert polymer matrix to recreate biological functions. Understanding the growth and spatial configuration of cellular populations within a matrix is crucial to predicting and improving their responsive potential and functionality. Here, this work investigates the growth, spatial distribution, and photosynthetic productivity of eukaryotic microalga Chlamydomonas reinhardtii (C. reinhardtii) in three-dimensionally shaped hydrogels in dependence of geometry and size. The embedded C. reinhardtii cells photosynthesize and form confined cell clusters, which grow faster when located close to the ELM periphery due to favorable gas exchange and light conditions. Taking advantage of location-specific growth patterns, this work successfully designs and prints photosynthetic ELMs with increased CO2 capturing rate, featuring high surface to volume ratio. This strategy to control cell growth for higher productivity of ELMs resembles the already established adaptations found in multicellular plant leaves.

Emergent Biological Endurance Depends on Extracellular Matrix Composition of Three-Dimensionally Printed Escherichia coli Biofilms.

Biofilms are three-dimensional (3D) bacterial communities that exhibit a highly self-organized nature in terms of their composition and complex architecture. Bacteria in biofilms display emergent biological properties, such as resistance to antimicrobials and disinfectants that the individual planktonic cells lack. Bacterial biofilms possess specialized architectural features including unique extracellular matrix compositions and a distinct spatially patterned arrangement of cells and matrix components within the biofilm. It is unclear which of these architectural elements of bacterial biofilms lead to the development of their emergent biological properties. Here, we report a 3D printing-based technique for studying the emergent resistance behaviors of Escherichia coli biofilms as a function of their architecture. Cellulose and curli are the major extracellular-matrix components in E. coli biofilms. We show that 3D-printed biofilms expressing either curli alone or both curli and cellulose in their extracellular matrices show higher resistance to exposure against disinfectants than 3D prints expressing either cellulose alone or no biofilm-matrix components. The 3D-printed biofilms expressing cellulose and/or curli also show thicker anaerobic zones than nonbiofilm-forming E. coli 3D prints. Thus, the matrix composition plays a crucial role in the emergent spatial patterning and biological endurance of 3D-printed biofilms. In contrast, initial spatial distribution of bacterial density or curli-producing cells does not have an effect on biofilm resistance phenotypes. Further, these 3D-printed biofilms could be reversibly attached to different surfaces (bacterial cellulose, glass, and polystyrene) and display resistance to physical distortions by retaining their shape and structure. This physical robustness highlights their potential in applications including bioremediation, protective coatings against pathogens on medical devices, or wastewater treatment, among many others. This new understanding of the emergent behavior of bacterial biofilms could aid in the development of novel engineered living materials using synthetic biology and materials science approaches.

Hydrodynamic shear dissipation and transmission in lipid bilayers.

Vital biological processes, such as trafficking, sensing, and motility, are facilitated by cellular lipid membranes, which interact mechanically with surrounding fluids. Such lipid membranes are only a few nanometers thick and composed of a liquid crystalline structure known as the lipid bilayer. Here, we introduce an active, noncontact, two-point microrheology technique combining multiple optical tweezers probes with planar freestanding lipid bilayers accessible on both sides. We use the method to quantify both fluid slip close to the bilayer surface and transmission of fluid flow across the structure, and we use numerical simulations to determine the monolayer viscosity and the intermonolayer friction. We find that these physical properties are highly dependent on the molecular structure of the lipids in the bilayer. We compare ordered-phase with liquid disordered-phase lipid bilayers, and we find the ordered-phase bilayers to be 10 to 100 times more viscous but with 100 times less intermonolayer friction. When a local shear is applied by the optical tweezers, the ultralow intermonolayer friction results in full slip of the two leaflets relative to each other and as a consequence, no shear transmission across the membrane. Our study sheds light on the physical principles governing the transfer of shear forces by and through lipid membranes, which underpin cell behavior and homeostasis.

Reconstitution and functional characterization of the FtsH protease in lipid nanodiscs.

FtsH is a membrane-bound protease that plays a crucial role in proteolytic regulation of many cellular functions. It is universally conserved in bacteria and responsible for the degradation of misfolded or misassembled proteins. A recent study has determined the structure of bacterial FtsH in detergent micelles. To properly study the function of FtsH in a native-like environment, we reconstituted the FtsH complex into lipid nanodiscs. We found that FtsH in membrane scaffold protein (MSP) nanodiscs maintains its native hexameric conformation and is functionally active. We further investigated the effect of the lipid bilayer composition (acyl chain length, saturation, head group charge and size) on FtsH proteolytic activity. We found that the lipid acyl chain length influences AaFtsH activity in nanodiscs, with the greatest activity in a bilayer of di-C18:1 PC. We conclude that MSP nanodiscs are suitable model membranes for further in vitro studies of the FtsH protease complex.

The cytoplasmic domain of the AAA+ protease FtsH is tilted with respect to the membrane to facilitate substrate entry.

AAA+ proteases are degradation machines that use ATP hydrolysis to unfold protein substrates and translocate them through a central pore toward a degradation chamber. FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control. How substrates reach the FtsH central pore is an open key question that is not resolved by the available atomic structures of cytoplasmic and periplasmic domains. In this work, we used both negative stain TEM and cryo-EM to determine 3D maps of the full-length Aquifex aeolicus FtsH protease. Unexpectedly, we observed that detergent solubilization induces the formation of fully active FtsH dodecamers, which consist of two FtsH hexamers in a single detergent micelle. The striking tilted conformation of the cytosolic domain in the FtsH dodecamer visualized by negative stain TEM suggests a lateral substrate entrance between the membrane and cytosolic domain. Such a substrate path was then resolved in the cryo-EM structure of the FtsH hexamer. By mapping the available structural information and structure predictions for the transmembrane helices to the amino acid sequence we identified a linker of ∼20 residues between the second transmembrane helix and the cytosolic domain. This unique polypeptide appears to be highly flexible and turned out to be essential for proper functioning of FtsH as its deletion fully eliminated the proteolytic activity of FtsH.

Bioproduced Polymers Self-Assemble with Graphene Oxide into Nanocomposite Films with Enhanced Mechanical Performance.

Graphene oxide (GO) has recently been highlighted as a promising multipurpose two-dimensional material. However, free-standing graphene oxide films suffer from poor strength and flexibility, which limits scaling-up of production and lifetime structural robustness in applications. Inspired by the relationship between the organic and inorganic components of the hierarchical structure of nacre found in mollusk shells, we have fabricated self-assembled, layered graphene-based composite films. The organic phase of our composite is produced via environmentally friendly and economical methods based on bacterial production of γ-poly(glutamic acid) (PGA). Composite films made of GO, PGA, and divalent cations (Ca2+) were prepared through a slow solvent evaporation method at ambient temperature, resulting in a nacre-like layered structure. These biobased nanocomposite films showed impressive mechanical properties, which resulted from a synergistic combination of hydrogen bonding with the bacterially produced PGA and ionic bonding with calcium ions (Ca2+). The GO/PGA/Ca2+ composite films possessed a high strength of 150 ± 51.9 MPa and a high Young's modulus of 21.4 ± 8.7 GPa, which represents an increase of 120% and over 70% with respect to pure GO films. We provide rational design strategies for the production of graphene-based films with improved mechanical performance, which can be applied in filtration purification of wastewater in the paper, food, beverage, pigment, and pharmaceuticals industries, as well as for manufacturing of functional membranes and surface coatings.

Spiral Honeycomb Microstructured Bacterial Cellulose for Increased Strength and Toughness.

Natural materials, such as nacre and silk, exhibit both high strength and toughness due to their hierarchical structures highly organized at the nano-, micro-, and macroscales. Bacterial cellulose (BC) presents a hierarchical fibril structure at the nanoscale. At the microscale, however, BC nanofibers are distributed randomly. Here, BC self-assembles into a highly organized spiral honeycomb microstructure giving rise to a high tensile strength (315 MPa) and a high toughness value (17.8 MJ m-3), with pull-out and de-spiral morphologies observed during failure. Both experiments and finite-element simulations indicate improved mechanical properties resulting from the honeycomb structure. The mild fabrication process consists of an in situ fermentation step utilizing poly(vinyl alcohol), followed by a post-treatment including freezing-thawing and boiling. This simple self-assembly production process is highly scalable, does not require any toxic chemicals, and enables the fabrication of light, strong, and tough hierarchical composite materials with tunable shape and size.

Fibrous Flagellar Hairs of Chlamydomonas reinhardtii Do Not Enhance Swimming.

The flagella of Chlamydomonas reinhardtii possess fibrous ultrastructures of a nanometer-scale thickness known as mastigonemes. These structures have been widely hypothesized to enhance flagellar thrust; however, detailed hydrodynamic analysis supporting this claim is lacking. In this study, we present a comprehensive investigation into the hydrodynamic effects of mastigonemes using a genetically modified mutant lacking the fibrous structures. Through high-speed observations of freely swimming cells, we found the average and maximum swimming speeds to be unaffected by the presence of mastigonemes. In addition to swimming speeds, no significant difference was found for flagellar gait kinematics. After our observations of swimming kinematics, we present direct measurements of the hydrodynamic forces generated by flagella with and without mastigonemes. These measurements were conducted using optical tweezers, which enabled high temporal and spatial resolution of hydrodynamic forces. Through our measurements, we found no significant difference in propulsive flows due to the presence of mastigonemes. Direct comparison between measurements and fluid mechanical modeling revealed that swimming hydrodynamics were accurately captured without including mastigonemes on the modeled swimmer's flagella. Therefore, mastigonemes do not appear to increase the flagella's effective area while swimming, as previously thought. Our results refute the longstanding claim that mastigonemes enhance flagellar thrust in C. reinhardtii, and so, their function still remains enigmatic.

Artificial Cell Membranes Interfaced with Optical Tweezers: A Versatile Microfluidics Platform for Nanomanipulation and Mechanical Characterization.

Cell lipid membranes are the site of vital biological processes, such as motility, trafficking, and sensing, many of which involve mechanical forces. Elucidating the interplay between such bioprocesses and mechanical forces requires the use of tools that apply and measure piconewton-level forces, e.g., optical tweezers. Here, we introduce the combination of optical tweezers with free-standing lipid bilayers, which are fully accessible on both sides of the membrane. In the vicinity of the lipid bilayer, optical trapping would normally be impossible due to optical distortions caused by pockets of the solvent trapped within the membrane. We solve this by drastically reducing the size of these pockets via tuning of the solvent and flow cell material. In the resulting flow cells, lipid nanotubes are straightforwardly pushed or pulled and reach lengths above half a millimeter. Moreover, the controlled pushing of a lipid nanotube with an optically trapped bead provides an accurate and direct measurement of important mechanical properties. In particular, we measure the membrane tension of a free-standing membrane composed of a mixture of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) to be 4.6 × 10-6 N/m. We demonstrate the potential of the platform for biophysical studies by inserting the cell-penetrating trans-activator of transcription (TAT) peptide in the lipid membrane. The interactions between the TAT peptide and the membrane are found to decrease the value of the membrane tension to 2.1 × 10-6 N/m. This method is also fully compatible with electrophysiological measurements and presents new possibilities for the study of membrane mechanics and the creation of artificial lipid tube networks of great importance in intra- and intercellular communication.

3D Printing for the Fabrication of Biofilm-Based Functional Living Materials.

Bacterial biofilms are three-dimensional networks of cells entangled in a self-generated extracellular polymeric matrix composed of proteins, lipids, polysaccharides, and nucleic acids. Biofilms can establish themselves on virtually any accessible surface and lead to varying impacts ranging from infectious diseases to degradation of toxic chemicals. Biofilms exhibit high mechanical stiffness and are inherently tolerant to adverse conditions including the presence of antibiotics, pollutants, detergents, high temperature, changes in pH, etc. These features make biofilms resilient, which is beneficial for applications in dynamic environments such as bioleaching, bioremediation, materials production, and wastewater purification. We have recently described an easy and cost-effective method for 3D printing of bacteria and have extended this technology for 3D printing of genetically engineered Escherichia coli biofilms. Our 3D printing platform exploits simple alginate chemistry for printing of a bacteria-alginate bioink mixture onto calcium-containing agar surfaces, resulting in the formation of bacteria-encapsulating hydrogels with varying geometries. Bacteria in these hydrogels remain intact, spatially patterned, and viable for several days. Printing of engineered bacteria to produce inducible biofilms leads to formation of multilayered three-dimensional structures that can tolerate harsh chemical treatments. Synthetic biology and material science approaches provide the opportunity to append a wide range of useful functionalities to these 3D-printed biofilms. In this article, we describe the wide range of future applications possible for applying functional 3D-printed biofilms to the construction of living biofilm-derived materials in a large-scale and environmentally stable manner.

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter.

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced antibiotic resistance, which poses potential health dangers, but can also be beneficial for environmental applications such as purification of drinking water. The further development of anti-bacterial therapeutics and biofilm-inspired applications will require the development of reproducible, engineerable methods for biofilm creation. Recently, a novel method of biofilm preparation using a modified three-dimensional (3D) printer with a bacterial ink has been developed. This article describes the steps necessary to build this efficient, low-cost 3D bioprinter that offers multiple applications in bacterially-induced materials processing. The protocol begins with an adapted commercial 3D printer in which the extruder has been replaced with a bio-ink dispenser connected to a syringe pump system enabling a controllable, continuous flow of bio-ink. To develop a bio-ink suitable for biofilm printing, engineered Escherichia coli bacteria were suspended in a solution of alginate, so that they solidify in contact with a surface containing calcium. The inclusion of an inducer chemical within the printing substrate drives expression of biofilm proteins within the printed bio-ink. This method enables 3D printing of various spatial patterns composed of discrete layers of printed biofilms. Such spatially-controlled biofilms can serve as model systems and can find applications in multiple fields that have a wide-ranging impact on society, including antibiotic resistance prevention or drinking water purification, among others.

Is the Zero Reynolds Number Approximation Valid for Ciliary Flows?

Stokes equations are commonly used to model the hydrodynamic flow around cilia on the micron scale. The validity of the zero Reynolds number approximation is investigated experimentally with a flow velocimetry approach based on optical tweezers, which allows the measurement of periodic flows with high spatial and temporal resolution. We find that beating cilia generate a flow, which fundamentally differs from the stokeslet field predicted by Stokes equations. In particular, the flow velocity spatially decays at a faster rate and is gradually phase delayed at increasing distances from the cilia. This indicates that the quasisteady approximation and use of Stokes equations for unsteady ciliary flow are not always justified and the finite timescale for vorticity diffusion cannot be neglected. Our results have significant implications in studies of synchronization and collective dynamics of microswimmers.

Bacterially Produced, Nacre-Inspired Composite Materials.

The impressive mechanical properties of natural composites, such as nacre, arise from their multiscale hierarchical structures, which span from nano- to macroscale and lead to effective energy dissipation. While some synthetic bioinspired materials have achieved the toughness of natural nacre, current production methods are complex and typically involve toxic chemicals, extreme temperatures, and/or high pressures. Here, the exclusive use of bacteria to produce nacre-inspired layered calcium carbonate-polyglutamate composite materials that reach and exceed the toughness of natural nacre, while additionally exhibiting high extensibility and maintaining high stiffness, is introduced. The extensive diversity of bacterial metabolic abilities and the possibility of genetic engineering allows for the creation of a library of bacterially produced, cost-effective, and eco-friendly composite materials.

Stable Free-Standing Lipid Bilayer Membranes in Norland Optical Adhesive 81 Microchannels.

We report a simple, cost-effective, and reproducible method to form free-standing lipid bilayer membranes in microdevices made with Norland Optical Adhesive 81 (NOA81). Surface treatment with either alkylsilane or fluoroalkylsilane enables the self-assembly of stable 1,2-diphytanoyl-sn-glycero-3-phosphocholine 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC) membranes. Capacitance measurements are used to characterize the lipid bilayer and to follow its formation in real-time. With current recordings, we detect the insertion of single α-hemolysin pores into the bilayer membrane, demonstrating the possibility of using this device for single-channel electrophysiology sensing applications. Optical transparency of the device and vertical position of the lipid bilayer with respect to the microscope focal plane allows easy integration with other single-molecule techniques, such as optical tweezers. Therefore, this method to form long-lived lipid bilayers finds a wide range of applications, from sensing measurements to biophysical studies of lipid bilayers and associated proteins.

SMA-SH: Modified Styrene-Maleic Acid Copolymer for Functionalization of Lipid Nanodiscs.

Challenges in purification and subsequent functionalization of membrane proteins often complicate their biochemical and biophysical characterization. Purification of membrane proteins generally involves replacing the lipids surrounding the protein with detergent molecules, which can affect protein structure and function. Recently, it was shown that styrene-maleic acid copolymers (SMA) can dissolve integral membrane proteins from biological membranes into nanosized discs. Within these nanoparticles, proteins are embedded in a patch of their native lipid bilayer that is stabilized in solution by the amphipathic polymer that wraps the disc like a bracelet. This approach for detergent-free purification of membrane proteins has the potential to greatly simplify purification but does not facilitate conjugation of functional compounds to the membrane proteins. Often, such functionalization involves laborious preparation of protein variants and optimization of labeling procedures to ensure only minimal perturbation of the protein. Here, we present a strategy that circumvents several of these complications through modifying SMA by grafting the polymer with cysteamine. The reaction results in SMA that has solvent-exposed sulfhydrils (SMA-SH) and allows tuning of the coverage with SH groups. Size exclusion chromatography, dynamic light scattering, and transmission electron microscopy demonstrate that SMA-SH dissolves lipid bilayer membranes into lipid nanodiscs, just like SMA. In addition, we demonstrate that, just like SMA, SMA-SH solubilizes proteoliposomes into protein-loaded nanodiscs. We covalently modify SMA-SH-lipid nanodiscs using thiol-reactive derivatives of Alexa Fluor 488 and biotin. Thus, SMA-SH promises to simultaneously tackle challenges in purification and functionalization of membrane proteins.

Hydrodynamics Versus Intracellular Coupling in the Synchronization of Eukaryotic Flagella.

The influence of hydrodynamic forces on eukaryotic flagella synchronization is investigated by triggering phase locking between a controlled external flow and the flagella of C. reinhardtii. Hydrodynamic forces required for synchronization are over an order of magnitude larger than hydrodynamic forces experienced in physiological conditions. Our results suggest that synchronization is due instead to coupling through cell internal fibers connecting the flagella. This conclusion is confirmed by observations of the vfl3 mutant, with impaired mechanical connection between the flagella.

Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine.

ClpXP and other AAA+ proteases recognize, mechanically unfold, and translocate target proteins into a chamber for proteolysis. It is not known whether these remarkable molecular machines operate by a stochastic or sequential mechanism or how power strokes relate to the ATP-hydrolysis cycle. Single-molecule optical trapping allows ClpXP unfolding to be directly visualized and reveals translocation steps of ∼1-4 nm in length, but how these activities relate to solution degradation and the physical properties of substrate proteins remains unclear. By studying single-molecule degradation using different multidomain substrates and ClpXP variants, we answer many of these questions and provide evidence for stochastic unfolding and translocation. We also present a mechanochemical model that accounts for single-molecule, biochemical, and structural results for our observation of enzymatic memory in translocation stepping, for the kinetics of translocation steps of different sizes, and for probabilistic but highly coordinated subunit activity within the ClpX ring.

Conjugation of nanoparticles to proteins.

Nanoparticle-protein conjugates hold great promise in biomedical applications. Diverse strategies have been developed to link nanoparticles to proteins. This chapter describes a method to assemble and purify nanoparticle-protein conjugates. First, stable and biocompatible 1.5 nm gold nanoparticles are synthesized. Conjugation of the nanoparticle to the protein is then achieved via two different approaches that do not require heavy chemical modifications or cloning: cysteine-gold covalent bonding, or electrostatic attachment of the nanoparticle to charged groups of the protein. Co-functionalization of the nanoparticle with PEG thiols is recommended to help protein folding. Finally, structural characterization is performed with circular dichroism, as this spectroscopy technique has proven to be effective at examining protein secondary structure in nanoparticle-protein conjugates.