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.

Keywords: biochemical techniques and resources; biotechnology; gene expression and regulation.

Figure 1.. Methods of controlling transcription and translation with light discussed in this review.

Uncaging the (A) DNA or (B) mRNA template of a gene of interest with light allows for activation of transcription/translation. Whereas regulation of gene expression with light can be achieved by using (C) caged small molecules, nucleic acids, and proteins or (D) engineering naturally light-sensitive proteins.

Figure 2.

An illustration of the approximate wavelength of activation of a number of photocages (A) and engineered naturally light-sensitive proteins (B, with chromophores) discussed in this review. NIR = near-infrared, NP = nanoparticle.

Figure 3.. Attachment points of photocages onto DNA (X = H) or RNA (X = OH).

(A) Photocages have been attached to various positions on DNA/RNA strands to control function, including the phosphate backbone (1), in the backbone (2), on the nucleobase (3), and on the Watson–Crick face of the nucleobase (4). These photocages can be attached to double stranded (B) or single stranded (C) nucleic acids.

Figure 4.. Controlling gene expression by using naturally light-sensitive proteins.

(A) Protein modules that dimerise in response to light, represented here as Light-Activated Domains (LADs), have been fused to effector domains to create transcription factors that activate gene expression in the presence of light, but are inactivate in the absence of light. Gene expression is activated upon co-localisation of DNA-Binding Domains (DBD) with transActivation Domains (ADs) via a light-activated two-hybrid system (i), or via the co-localisation of inactive C- and N-terminal domains of a split protein and reconstitution of the active protein (ii). (B) Light-responsive two component systems (TCSs) are initiated when light is absorbed by the sensory domain of a histidine kinase, which stimulates/represses autophosphorylation of the kinases domains. Phosphorylated kinase domains transfer phosphate groups to downstream Transcription Factors (TF), which can then bind to consensus promoter sequences and activate gene expression. (C) Uncaging of the Jα helix in AsLOV2, when exposed to blue light, is used to reveal a shielded Nuclear Localisation Signal (NLS). The exposed NLS is recognised by the importin complex and AsLOV2 is transported into the nucleus. Gene expression can be regulated by fusing DBDs and ADs to AsLOV2, and controlling their nuclear localisation by exposing or shielding the NLS.