Controlling gene expression with light: a multidisciplinary endeavour

Abstract

The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.

Optochemical Control of Bacterial Gene Expression: Novel Photocaged Compounds for Different Promoter Systems

“… [2] Mostly, genetically encoded light‐sensitive photoreceptors, which have their natural origin in plants or fungi (e. g. LOV domains, phytochromes or other photosensory proteins), are used to construct recombinant control elements applicable for activating or repressing transcription. [ 1b , 3 ] In contrast, light‐activatable molecules consist of a bioactive component and a photoremovable protecting group, retaining it in an inactive state until irradiation with a certain wavelength restores its bioactivity by photochemically initiated covalent bond cleavage. [4] Different types of biomolecules as nucleic acids, peptides or small inducer molecules can be targeted with this method to achieve light‐regulated gene expression.…”

“… [4] Different types of biomolecules as nucleic acids, peptides or small inducer molecules can be targeted with this method to achieve light‐regulated gene expression. [ 1b , 5 ] However, there is still a limited number of small molecule‐inducible gene expression systems available, which have been addressed by light‐regulation. Most of them were targeted in eukaryotic cells by ecdysone, [6] doxycycline, [7] tamoxifen, [8] cyclofen‐OH, [9] methionine, [10] and copper.…”

Controlling Synthetic Cell-Cell Communication

“…One caveat to the current light-activated DNA templates, and most other synthetic light-activated systems on offer, stems from the use of UV light, which can be cytotoxic at high doses and has little tissue penetration ( Olejniczak et al, 2015 ); therefore, there is a need for light-activated systems that respond to longer wavelengths of light. Alternative optogenetic systems such as light-activated TFs ( Jayaraman et al, 2018 ) or two-component systems ( Zhang et al, 2020 ) can also be used to control cell-free gene expression with more red-shifted wavelengths of light, and other light-activated systems that work well in bacteria may transition into CFPS ( Hartmann et al, 2020 ), although this has yet to be realised. Light-responsive gene expression could be used to controllably produce and release small molecules or proteins and might be applied in tissue engineering efforts to spatially control morphogen gradients and direct tissue differentiation.…”

Double-Lariat Caged Morpholino Oligonucleotides for Optical Gene Silencing

“…1,2 Because specific tissues can be illuminated at precise timepoints, photoactivatable reagents are well-suited for inducing molecular perturbations in whole organisms with spatial and temporal control. 3,4 These technologies are particularly useful when applied in optically transparent model organisms that develop ex utero such as zebrafish, 5 sea urchins, 6 and ascidians. 7 Oligonucleotide-based reagents are especially versatile probes as they can be readily designed to specifically target any gene, 8,9 and phosphorodiamidate morpholino oligonucleotides (MOs) have been most commonly used to inhibit gene expression in vivo.…”