Preface

Nine years after the seminal review The optogenetic catechism by Gero Miesenböck¹ , optogenetic tools have expanded its application not only in neuroscience but also in cell physiology. It has allowed a spatiotemporal quantitative approach to interrogating biological processes such as cell trafficking, cell signalling and the discovery of new biological mechanisms. Owing to this surge of new applications of optogenetics in cell biology, we thought that it was the time for a survey of what has been done and what remains to be explored.

Optogenetic development needs convergent efforts by chemists, physicists and biologists and these three disciplines are well represented amongst the authors. We decided to organize the book in three parts, which correspond to the major research territories in the optogenetic landscape: light taming, light-emitting sensors and light-driven actuators.

Illumination and signal recording are the heart of optogenetics. Light needs to be tamed for sensitivity, faster recording and better resolution to improve our understanding of life mechanisms. Different approaches are used to achieve these goals and today living biological systems can be observed in three dimensions (3D), at subsecond resolution and at the diffraction limit or below. The first chapter lays the ground for illuminating methods and discusses light-sheet fluorescence microscopy (LSFM), which allows very fast recording of signals in a large volume. The combination of optogenetic tools with LSFM opens up the possibility of recording fluorescent signals from thousands of individual cells in less than 1 s. This allows the intricate study of cell signalling at the organ or animal scale with single-cell resolution and provides access to signalling patterns, spreading and feedback loop operation in living animals. This now leads to the need to develop computational methods to process and analyse massive datasets produced by such readout techniques. The second chapter addresses the adjustment of super-resolution microscopy to optogenetics. Indeed, super-resolution microscopy of living systems remains a challenge, even though it is essential to stretch the limits for the analysis of signalling spreading inside the cell.

Light-emitting sensors transform physiological signals into fluorescent signals. Their development revolutionises cell biology, and a large toolbox of fluorescent proteins able to reveal protein abundance, localization, dynamics and activity with unprecedented temporal and spatial resolution is now available. Each one is peculiar and specific to the signal to be recorded; however, two major families of fluorescent proteins are used: one is derived from canonical fluorescent proteins and the other from non-fluorescent probes (fluorogens) that become fluorescent only when complexed to a fluorogen-activating protein (FAP). Chapters 3 and 4 address major developments in these two families and give precise and practical examples for each of them. The spectrum of available wavelengths for absorption and emission is still expending, making multiplexing easier and signalling network recording possible.

The last section is dedicated to actuators. The ultimate proof for the comprehension of a phenomenon is often the possibility of initiating and manipulating the signal(s) involved. Light-driven actuators achieve this goal. In order to turn a protein into a light-responsive entity, it is possible to rely either on light-sensing proteins already characterized in a specific organism or on the addition of a light-sensitive module to a protein of interest. In most cases, under illumination, the associated chromophore isomerizes and induces an overall conformational change of the protein, which can be rerouted to manipulate protein activity.^2,3  Light-sensitive modules are continuously being improved for dynamic response and light sensitivity and adapted for the regulation of a wide range of proteins. The last part of this book presents specific examples of actuators dedicated to cell biology. Because of space constraints, it was not possible to be exhaustive, but we feel that the sampling we have made will give the flavour of what is possible with some examples presented in practical details. Chapter 6 gives an overview of the chromophore light inactivation (CALI) method to inactivate proteins. Chapters 5, 7 and 8 present different examples of signal transduction light manipulation and Chapter 10 outlines a general method to control the activity of receptor tyrosine kinases. Chapter 9 reports light control of transcription to discriminate oscillatory versus sustained gene expression during embryonic development. Finally, Chapter 11 gives practical examples of light-controlled mechanotransduction.

In conclusion, we would like to express our strongest thanks to Evelyne Sage, Emeritus Research Director at the Curie Institute and co-Editor of the book series, who initiated this project and encouraged us throughout the preparation of this book.

Sophie Vriz and Takeaki Ozawa