Intracellular light-activation of riboswitch activity

Gene Regulation by a Kinetic Riboswitch with Negative Feedback Loop

Understanding the folding behaviors and cellular roles is important to fully illuminate functions of riboswitches in vivo. Since riboswitches act without the need for protein factors, RNA structure prediction methods are ideally suited for computationally analyzing their cellular activities. Here, a helix-based RNA folding theory is used to predict the cotranscriptional folding pathways of the flavin mononucleotide (FMN)-binding riboswitch from Bacillus subtilis (B. subtilis) under different conditions. The results show that the efficient function is determined by a balance between the transcription speed, pausing, and the binding rates of the metabolite. According to the predicted behaviors, a general kinetic model is established to investigate how the riboswitch couples sensing and regulatory functions to help bacteria respond to environmental changes at the system levels.

Optogenetic Tools for Regulating RNA Metabolism and Functions

RNA molecules play a vital role in linking genetic information with various cellular processes. In recent years, a variety of optogenetic tools have been engineered for regulating cellular RNA metabolism and functions. These highly desirable tools can offer non-intrusive control with spatial precision, remote operation, and biocompatibility. Here, we would like to review these currently available approaches that can regulate RNAs with light: from non-genetically encodable chemically modified oligonucleotides to genetically encoded RNA aptamers that recognize photosensitive small-molecule or protein ligands. Some key applications of these optogenetic tools will also be highlighted to illustrate how they have been used for regulating all aspects of the RNA life cycle: from RNA synthesis, maturation, modification, and translation to their degradation, localization, and phase separation control. Some current challenges and potential practical utilizations of these RNA optogenetic tools will also be discussed.

Development of label-free light-controlled gene expression technologies using mid-IR and terahertz light

Gene expression is a fundamental process that regulates diverse biological activities across all life stages. Given its vital role, there is an urgent need to develop innovative methodologies to effectively control gene expression. Light-controlled gene expression is considered a favorable approach because of its ability to provide precise spatiotemporal control. However, current light-controlled technologies rely on photosensitive molecular tags, making their practical use challenging. In this study, we review current technologies for light-controlled gene expression and propose the development of label-free light-controlled technologies using mid-infrared (mid-IR) and terahertz light.

Translational control of gene function through optically regulated nucleic acids

Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.

Light-controllable RNA-protein devices for translational regulation of synthetic mRNAs in mammalian cells

The photo-regulation of transgene expression is one effective approach in mammalian synthetic biology due to its high spatial and temporal resolution. While DNAs are mainly used as vectors, modified RNAs (modRNAs) are also useful for medical applications of synthetic biology, because they can avoid insertional mutagenesis and immunogenicity. However, the optogenetic control of modRNA-delivered transgenes is much more difficult than that of DNA-delivered transgenes. Here, we develop two types of photo-controllable translational activation systems that are compatible with modRNAs. One is composed of a heterodimerization domain-fused split translational activator protein and a photocaged heterodimerizer. The other is composed of a destabilizing domain-fused translational activator protein and a photocaged stabilizer. The destabilized type can be used for not only translational activation but also translational repression of the modRNAs. These photo-controllable translation systems will expand the application of mammalian synthetic biology research.

Photochemical control of bacterial gene expression based on trans encoded genetic switches

Controlling gene expression by light with fine spatiotemporal resolution not only allows understanding and manipulating fundamental biological processes but also fuels the development of novel therapeutic strategies. In complement to exploiting optogenetic tools, photochemical strategies mostly rely on the incorporation of photo-responsive small molecules into the corresponding biomacromolecular scaffolds. Therefore, generally large synthetic effort is required and the switching of gene expression in both directions within a single system remains a challenge. Here, we report a trans encoded ribo-switch, which consists of an engineered tRNA mimicking structure (TMS), under control of small photo-switchable signalling molecules. The signalling molecules consist of two amino glycoside molecules that are connected via an azobenzene unit. The light responsiveness of our system originates from the photo-switchable noncovalent interactions between the signalling molecule and the TMS switch, leading to the demonstration of photochemically controlled expression of two different genes. We believe that this modular design will provide a powerful platform for controlling the expression of other functional proteins with high spatiotemporal resolution employing light as a stimulus.

Controlling gene expression with light: a multidisciplinary endeavour

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.

The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research

The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.

Regulation of mRNA translation by a photoriboswitch

Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)-a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.

Light-triggered release of photocaged therapeutics - Where are we now?

The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.

Optochemical control of gene expression by photocaged guanine and riboswitches

A photocaged guanine was synthesized to optically control gene expression in cells using synthetic riboswitches.

Light Control of Protein Solubility Through Isoelectric Point Modulation

We previously described the photoactivated depot or PAD approach that allows for the light control of therapeutic protein release. This approach relies on the ability to use light to change a protein's solubility. Traditionally this was accomplished by linking the protein to an insoluble but injectable polymer via a light cleaved linker. This allows the injected material to remain at the site of injection, until transcutaneous irradiation breaks the link between polymer and protein, permitting the protein to be absorbed. However, there are multiple problems associated with polymer based approaches: The polymer makes up a majority of the material, making it inefficient. In addition, after protein release, the polymer has to be cleared from the body, a significant design challenge. In this work, we create materials that form photoactivated depots of insulin without the need for polymers, by linking photolysis to an isoelectric point shift, which itself is linked to a solubility shift. Specifically, we linked basic groups to insulin via a light cleaved linker. These shift the normal pI of insulin from 5.4 to approximately 7. The result of this incorporation are materials that are completely soluble in mildly acidic solutions but precipitate upon injection into a pH 7 environment, i.e., the skin. We successfully synthesized four such modified insulins, demonstrating that their pI values were shifted in the expected manner. We then analyzed one of them, P2-insulin, in detail, demonstrating that it behaves as designed: It is soluble in a formulation pH of 4, but precipitates at pH 7.2, its approximate pI value. Upon irradiation, the photocleavable link to insulin is broken, and completely native and soluble insulin is released from the depot in a well behaved, first order fashion. These materials are 90% therapeutic, form completely soluble and injectable formulations in mildly acidic conditions, form insoluble depots at neutral pH, efficiently release soluble protein from these depots when irradiated, and leave behind only small easily absorbed molecules after irradiation. As such they approach ideality for photoactivated depot materials.

An open-hardware platform for optogenetics and photobiology

In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.

Nitrodibenzofuran: A One- and Two-Photon Sensitive Protecting Group That Is Superior to Brominated Hydroxycoumarin for Thiol Caging in Peptides

Photoremovable protecting groups are important for a wide range of applications in peptide chemistry. Using Fmoc-Cys(Bhc-MOM)-OH, peptides containing a Bhc-protected cysteine residue can be easily prepared. However, such protected thiols can undergo isomerization to a dead-end product (a 4-methylcoumarin-3-yl thioether) upon photolysis. To circumvent that photoisomerization problem, we explored the use of nitrodibenzofuran (NDBF) for thiol protection by preparing cysteine-containing peptides where the thiol is masked with an NDBF group. This was accomplished by synthesizing Fmoc-Cys(NDBF)-OH and incorporating that residue into peptides by standard solid-phase peptide synthesis procedures. Irradiation with 365 nm light or two-photon excitation with 800 nm light resulted in efficient deprotection. To probe biological utility, thiol group uncaging was carried out using a peptide derived from the protein K-Ras4B to yield a sequence that is a known substrate for protein farnesyltransferase; irradiation of the NDBF-caged peptide in the presence of the enzyme resulted in the formation of the farnesylated product. Additionally, incubation of human ovarian carcinoma (SKOV3) cells with an NDBF-caged version of a farnesylated peptide followed by UV irradiation resulted in migration of the peptide from the cytosol/Golgi to the plasma membrane due to enzymatic palmitoylation. Overall, the high cleavage efficiency devoid of side reactions and significant two-photon cross-section of NDBF render it superior to Bhc for thiol group caging. This protecting group should be useful for a plethora of applications ranging from the development of light-activatable cysteine-containing peptides to the development of light-sensitive biomaterials.

Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme

Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.

Photocaged DNAzymes as a general method for sensing metal ions in living cells

DNAzymes, which are sequences of DNA with catalytic activity, have been demonstrated as a potential platform for sensing a wide range of metal ions. Despite their significant promise, cellular sensing using DNAzymes has however been difficult, mainly because of the "always-on" mode of first-generation DNAzyme sensors. To overcome this limitation, a photoactivatable (or photocaged) DNAzyme was designed and synthesized, and its application in sensing Zn(II) in living cells was demonstrated. In this design, the adenosine ribonucleotide at the scissile position of the 8-17 DNAzyme was replaced by 2'-O-nitrobenzyl adenosine, rendering the DNAzyme inactive and thus allowing its delivery into cells intact, protected from nonspecific degradation within cells. Irradiation at 365 nm restored DNAzyme activity, thus allowing the temporal control over the sensing activity of the DNAzyme for metal ions. The same strategy was also applied to the GR-5 DNAzyme for the detection of Pb(II), thus demonstrating the possible scope of the method.