Physical Plasma Membrane Perturbation Using Subcellular Optogenetics Drives Integrin-Activated Cell Migration

Synthetic Lipid Biology

Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.

T cells go with the flow: aquaporin 4 is required for full T-cell activation

Proximal T-cell receptor signaling and subsequent T cell activation was reduced downstream of anti-CD3/CD28 ligation through small molecule inhibition of the water channel aquaporin 4.

Modelling the role of membrane mechanics in cell adhesion on titanium oxide nanotubes

Titanium surface treated with titanium oxide nanotubes was used in many studies to quantify the effect of surface topography on cell fate. However, the predicted optimal diameter of nanotubes considerably differs among studies. We propose a model that explains cell adhesion to a nanostructured surface by considering the deformation energy of cell protrusions into titanium nanotubes and the adhesion to the surface. The optimal surface topology is defined as a geometry that gives the membrane a minimum energy shape. A dimensionless parameter, the cell interaction index, was proposed to describe the interplay between the cell membrane bending, the intrinsic curvature, and the strength of cell adhesion. Model simulation shows that an optimal nanotube diameter ranging from 20 nm to 100 nm (cell interaction index between 0.2 and 1, respectively) is feasible within a certain range of parameters describing cell membrane adhesion and bending. The results indicate a possibility to tune the topology of a nanostructural surface in order to enhance the proliferation and differentiation of cells mechanically compatible with the given surface geometry while suppressing the growth of other mechanically incompatible cells.

Cell Repolarization: A Bifurcation Study of Spatio-Temporal Perturbations of Polar Cells

The intrinsic polarity of migrating cells is regulated by spatial distributions of protein activity. Those proteins (Rho-family GTPases, such as Rac and Rho) redistribute in response to stimuli, determining the cell front and back. Reaction-diffusion equations with mass conservation and positive feedback have been used to explain initial polarization of a cell. However, the sensitivity of a polar cell to a reversal stimulus has not yet been fully understood. We carry out a PDE bifurcation analysis of two polarity models to investigate routes to repolarization: (1) a single-GTPase ("wave-pinning") model and (2) a mutually antagonistic Rac-Rho model. We find distinct routes to reversal in (1) vs. (2). We show numerical simulations of full PDE solutions for the RD equations, demonstrating agreement with predictions of the bifurcation results. Finally, we show that simulations of the polarity models in deforming 1D model cells are consistent with biological experiments.

Recent developments in membrane curvature sensing and induction by proteins

BACKGROUND

Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding.

SCOPE OF REVIEW

We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins.

MAJOR CONCLUSIONS

Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood.

GENERAL SIGNIFICANCE

The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.

Optogenetic Control of RhoA to Probe Subcellular Mechanochemical Circuitry

Spatiotemporal localization of protein function is essential for physiological processes from subcellular to tissue scales. Genetic and pharmacological approaches have played instrumental roles in isolating molecular components necessary for subcellular machinery. However, these approaches have limited capabilities to reveal the nature of the spatiotemporal regulation of subcellular machineries like those of cytoskeletal organelles. With the recent advancement of optogenetic probes, the field now has a powerful tool to localize cytoskeletal stimuli in both space and time. Here, we detail the use of tunable light-controlled interacting protein tags (TULIPs) to manipulate RhoA signaling in vivo. This is an optogenetic dimerization system that rapidly, reversibly, and efficiently directs a cytoplasmic RhoGEF to the plasma membrane for activation of RhoA using light. We first compare this probe to other available optogenetic systems and outline the engineering logic for the chosen recruitable RhoGEFs. We also describe how to generate the cell line, spatially control illumination, confirm optogenetic control of RhoA, and mechanically induce cell-cell junction deformation in cultured tissues. Together, these protocols detail how to probe the mechanochemical circuitry downstream of RhoA signaling. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of a stable cell line expressing TULIP constructs Basic Protocol 2: Preparation of collagen substrate for imaging Basic Protocol 3: Transient transfection for visualization of downstream effectors Basic Protocol 4: Calibration of spatial illumination Basic Protocol 5: Optogenetic activation of a region of interest.

Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways

Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events.

Adaptive viscoelasticity of epithelial cell junctions: from models to methods

Epithelial morphogenesis relies on constituent cells' ability to finely tune their mechanical properties. Resulting elastic-like and viscous-like behaviors arise from mechanochemical signaling coordinated spatiotemporally at cell-cell interfaces. Direct measurement of junction rheology can mechanistically dissect mechanical deformations and their molecular origins. However, the physical basis of junction viscoelasticity has only recently become experimentally tractable. Pioneering studies have uncovered exciting findings on the nature of contractile forces and junction deformations, inspiring a fundamentally new way of understanding morphogenesis. Here, we discuss novel techniques that directly test junctional mechanics and describe the relevant Vertex Models, and adaptations thereof, capturing these data. We then present the concept of adaptive tissue viscoelasticity, revealed by optogenetic junction manipulation. Finally, we offer future perspectives on this rapidly evolving field describing the material basis of tissue morphogenesis.

Lights up on organelles: Optogenetic tools to control subcellular structure and organization

Since the neurobiological inception of optogenetics, light-controlled molecular perturbations have been applied in many scientific disciplines to both manipulate and observe cellular function. Proteins exhibiting light-sensitive conformational changes provide researchers with avenues for spatiotemporal control over the cellular environment and serve as valuable alternatives to chemically inducible systems. Optogenetic approaches have been developed to target proteins to specific subcellular compartments, allowing for the manipulation of nuclear translocation and plasma membrane morphology. Additionally, these tools have been harnessed for molecular interrogation of organelle function, location, and dynamics. Optogenetic approaches offer novel ways to answer fundamental biological questions and to improve the efficiency of bioengineered cell factories by controlling the assembly of synthetic organelles. This review first provides a summary of available optogenetic systems with an emphasis on their organelle-specific utility. It then explores the strategies employed for organelle targeting and concludes by discussing our perspective on the future of optogenetics to control subcellular structure and organization. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology.

Biomechanical Contributions to Macrophage Activation in the Tumor Microenvironment

Alterations in extracellular matrix composition and organization are known to promote tumor growth and metastatic progression in breast cancer through interactions with tumor cells as well as stromal cell populations. Macrophages display a spectrum of behaviors from tumor-suppressive to tumor-promoting, and their function is spatially and temporally dependent upon integrated signals from the tumor microenvironment including, but not limited to, cytokines, metabolites, and hypoxia. Through years of investigation, the specific biochemical cues that recruit and activate tumor-promoting macrophage functions within the tumor microenvironment are becoming clear. In contrast, the impact of biomechanical stimuli on macrophage activation has been largely underappreciated, however there is a growing body of evidence that physical cues from the extracellular matrix can influence macrophage migration and behavior. While the complex, heterogeneous nature of the extracellular matrix and the transient nature of macrophage activation make studying macrophages in their native tumor microenvironment challenging, this review highlights the importance of investigating how the extracellular matrix directly and indirectly impacts tumor-associated macrophage activation. Additionally, recent advances in investigating macrophages in the tumor microenvironment and future directions regarding mechano-immunomodulation in cancer will also be discussed.

Light-Inducible Generation of Membrane Curvature in Live Cells with Engineered BAR Domain Proteins

Nanoscale membrane curvature is now understood to play an active role in essential cellular processes such as endocytosis, exocytosis, and actin dynamics. Previous studies have shown that membrane curvature can directly affect protein function and intracellular signaling. However, few methods are able to precisely manipulate membrane curvature in live cells. Here, we report the development of a new method of generating nanoscale membrane curvature in live cells that is controllable, reversible, and capable of precise spatial and temporal manipulation. For this purpose, we make use of Bin/Amphiphysin/Rvs (BAR) domain proteins, a family of well-studied membrane-remodeling and membrane-sculpting proteins. Specifically, we engineered two optogenetic systems, opto-FBAR and opto-IBAR, that allow light-inducible formation of positive and negative membrane curvature, respectively. Using opto-FBAR, blue light activation results in the formation of tubular membrane invaginations (positive curvature), controllable down to the subcellular level. Using opto-IBAR, blue light illumination results in the formation of membrane protrusions or filopodia (negative curvature). These systems present a novel approach for light-inducible manipulation of nanoscale membrane curvature in live cells.

Principles and applications of optogenetics in developmental biology

The development of multicellular organisms is controlled by highly dynamic molecular and cellular processes organized in spatially restricted patterns. Recent advances in optogenetics are allowing protein function to be controlled with the precision of a pulse of laser light in vivo, providing a powerful new tool to perturb developmental processes at a wide range of spatiotemporal scales. In this Primer, we describe the most commonly used optogenetic tools, their application in developmental biology and in the nascent field of synthetic morphogenesis.