Engineering strain-sensitive yellow fluorescent protein

Molecular Force Sensors for Biological Application

The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.

Mechano-Chemical Coupling in Hydra Regeneration and Patterning

The freshwater cnidarian Hydra can regenerate from wounds, small tissue fragments and even from aggregated cells. This process requires the de novo development of a body axis and oral-aboral polarity, a fundamental developmental process that involves chemical patterning and mechanical shape changes. Gierer and Meinhardt recognized that Hydra's simple body plan and amenability to in vivo experiments make it an experimentally and mathematically tractable model to study developmental patterning and symmetry breaking. They developed a reaction-diffusion model, involving a short-range activator and a long-range inhibitor, which successfully explained patterning in the adult animal. In 2011, HyWnt3 was identified as a candidate for the activator. However, despite the continued efforts of both physicists and biologists, the predicted inhibitor remains elusive. Furthermore, the Gierer-Meinhardt model cannot explain de novo axis formation in cellular aggregates that lack inherited tissue polarity. The aim of this review is to synthesize the current knowledge on Hydra symmetry breaking and patterning. We summarize the history of patterning studies and insights from recent biomechanical and molecular studies, and highlight the need for continued validation of theoretical assumptions and collaboration across disciplinary boundaries. We conclude by proposing new experiments to test current mechano-chemical coupling models and suggest ideas for expanding the Gierer-Meinhardt model to explain de novo patterning, as observed in Hydra aggregates. The availability of a fully sequenced genome, transgenic fluorescent reporter strains, and modern imaging techniques, that enable unprecedented observation of cellular events in vivo, promise to allow the community to crack Hydra's secret to patterning.

Molecular Force Measurement with Tension Sensors

The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. In this review, we discuss the physical principles, advantages, and limitations of this increasingly popular method. By highlighting current examples from the literature, we demonstrate how molecular tension sensors can be utilized to obtain access to previously unappreciated biophysical parameters that define the propagation of mechanical forces on molecular scales. We discuss how the methodology can be further developed and provide a perspective on how the technique could be applied to uncover entirely novel aspects of mechanobiology in the future.

From Molecules to Polymers-Harnessing Inter- and Intramolecular Interactions to Create Mechanochromic Materials

The development of mechanophores as building blocks that serve as predefined weak linkages has enabled the creation of mechanoresponsive and mechanochromic polymer materials, which are interesting for a range of applications including the study of biological specimens or advanced security features. In typical mechanophores, covalent bonds are broken when polymers that contain these chemical motifs are exposed to mechanical forces, and changes of the optical properties upon bond scission can be harnessed as a signal that enables the detection of applied mechanical stresses and strains. Similar chromic effects upon mechanical deformation of polymers can also be achieved without relying on the scission of covalent bonds. The dissociation of motifs that feature directional noncovalent interactions, the disruption of aggregated molecules, and conformational changes in molecules or polymers constitute an attractive element for the design of mechanoresponsive and mechanochromic materials. In this article, it is reviewed how such alterations of molecules and polymers can be exploited for the development of mechanochromic materials that signal deformation without breaking covalent bonds. Recent illustrative examples are highlighted that showcase how the use of such mechanoresponsive motifs enables the visual mapping of stresses and damage in a reversible and highly sensitive manner.

Yellow fluorescent protein-based label-free tension sensors for monitoring integrin tension

Yellow fluorescent protein serves as a label-free tension sensor to monitor integrin tension.

Recent Advances in Development of Genetically Encoded Fluorescent Sensors

Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.

Self-reporting Polymeric Materials with Mechanochromic Properties

The mechanical transduction of force onto molecules is an essential feature of many biological processes that results in the senses of touch and hearing, gives important cues for cellular interactions and can lead to optically detectable signals, such as a change in colour, fluorescence or chemoluminescence. Polymeric materials that are able to visually indicate deformation, stress, strain or the occurrence of microdamage draw inspiration from these biological events. The field of self-reporting (or self-assessing) materials is reviewed. First, mechanochromic events in nature are discussed, such as the formation of bruises on skin, the bleeding of a wound, or marine glow caused by dinoflagellates. Then, materials based on force-responsive mechanophores, such as spiropyrans, cyclobutanes, cyclooctanes, Diels–Alder adducts, diarylbibenzofuranone and bis(adamantyl)-1,2-dioxetane are reviewed, followed by mechanochromic blends, chromophores stabilised by hydrogen bonds, and pressure sensors based on ionic interactions between fluorescent dyes and polyelectrolyte brushes. Mechanobiochemistry is introduced as an important tool to create self-reporting hybrid materials that combine polymers with the force-responsive properties of fluorescent proteins, protein FRET pairs, and other biomacromolecules. Finally, dye-filled microcapsules, microvascular networks, and hollow fibres are demonstrated to be important technologies to create damage-indicating coatings, self-reporting fibre-reinforced composites and self-healing materials.

Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters

Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e.g., chloride and calcium), redox indicators, membrane potential, temperature, pressure, and molecular crowding. We demonstrate that these fluroescent protein-based sensors have a shared history of concepts and development strategies, and we highlight the most original concepts used to date. We believe that the understanding and application of these various concepts will pave the road for the development of future GE sensors and lead to new breakthroughs in bioimaging.

How to Measure Molecular Forces in Cells: A Guide to Evaluating Genetically-Encoded FRET-Based Tension Sensors

The ability of cells to sense and respond to mechanical forces is central to a wide range of biological processes and plays an important role in numerous pathologies. The molecular mechanisms underlying cellular mechanotransduction, however, have remained largely elusive because suitable methods to investigate subcellular force propagation were missing. Here, we review recent advances in the development of biosensors that allow molecular force measurements. We describe the underlying principle of currently available techniques and propose a strategy to systematically evaluate new Förster resonance energy transfer (FRET)-based biosensors.

The detection and role of molecular tension in focal adhesion dynamics

Cells are exquisitely sensitive to the mechanical nature of their environment, including applied force and the stiffness of the extracellular matrix (ECM). Recent evidence has shown that these variables are critical regulators of diverse processes mediating embryonic development, adult tissue physiology, and many disease states, including cancer, atherosclerosis, and myopathies. Often, detection of mechanical stimuli is mediated by the structures that link cells that surround ECM, the focal adhesions (FAs). FAs are intrinsically force sensitive and display altered dynamics, structure, and composition in response to applied load. While much progress has been made in determining the proteins that localize to and regulate the formation of these structures, less is known about the role of tension across specific proteins in this process. A recently developed class of force-sensitive biosensors is enabling a greater understanding of the molecular bases of cellular mechanosensitivity and cell migration.

Joining forces: integrating the mechanical and optical single molecule toolkits

Combining single molecule force measurements with fluorescence detection opens up exciting new possibilities for the characterization of mechanoresponsive molecules in Biology and Materials Science.

Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure

Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and dynamics of living cells. Despite being an important factor in many biological processes, the development of an indicator for the physicochemical state of water, such as pressure, viscosity and temperature, however, has been neglected. We here found a novel mutation that dramatically enhances the pressure dependency of the yellow fluorescent protein (YFP) by inserting several glycines into it. The crystal structure of the mutant showed that the tyrosine near the chromophore flipped toward the outside of the β-can structure, resulting in the entry of a few water molecules near the chromophore. In response to changes in hydrostatic pressure, a spectrum shift and an intensity change of the fluorescence were observed. By measuring the fluorescence of the YFP mutant, we succeeded in measuring the intracellular pressure change in living cell. This study shows a new strategy of design to engineer fluorescent protein indicators to sense hydrostatic pressure.

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, “RCaMPs,” engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca²⁺-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca²⁺]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca²⁺ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.