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Cells receive enormous amounts of information from their environment. How they act on this information—by migrating, expressing genes, or relaying signals to other cells—comprises much of the regulatory and self-organizational complexity found across biology. The “parts list” involved in cell signaling is generally well established, but how do these parts work together to decode signals and produce appropriate responses? This fundamental question is increasingly being addressed with optogenetic tools: light-sensitive proteins that enable biologists to manipulate the interaction, localization, and activity state of proteins with high spatial and temporal precision. In this review, we summarize how optogenetics is being used in the pursuit of an answer to this question, outlining the current suite of optogenetic tools available to the researcher and calling attention to studies that increase our understanding of and improve our ability to engineer biology.

Protein clusters and condensates are pervasive in mammalian signaling. Yet how the signaling capacity of higher-order assemblies differs from simpler forms of molecular organization is still poorly understood. Here, we present an optogenetic approach to switch between light-induced clusters and simple protein heterodimers with a single point mutation. We apply this system to study how clustering affects signaling from the kinase Zap70 and its substrate LAT, proteins that normally form membrane-localized clusters during T cell activation. We find that light-induced clusters of LAT and Zap70 trigger potent activation of downstream signaling pathways even in non-T cells, whereas one-to-one dimers do not. We provide evidence that clusters harbor a local positive feedback loop between three components: Zap70, LAT, and Src-family kinases that bind to phosphorylated LAT and further activate Zap70. Overall, our study provides evidence for a specific role of protein condensates in cell signaling, and identifies a simple biochemical circuit that can robustly sense protein oligomerization state.Highlights-A general system for studying the role of protein clusters versus dimers.-Membrane clusters of the kinase Zap70 and its substrate LAT trigger potent downstream signaling.-Clustering Zap70 with LAT is required for full activation of Zap70 kinase activity.-A positive feedback loop connects phosphorylated LAT to Zap70 activation via Src-family kinases.

Protein coacervates serve as hubs to concentrate and sequester proteins and nucleotides and thus function as membrane-less organelles to manipulate cell physiology. We have engineered a coacervating protein to create tunable, synthetic membrane-less organelles that assemble in response to a single pulse of light. Coacervation is driven by the intrinsically disordered RGG domain from the protein LAF-1, and opto-responsiveness is coded by the protein PhoCl which cleaves in response to 405 nm light. We developed a fusion protein containing a solubilizing maltose binding protein domain, PhoCl, and two copies of the RGG domain. Several seconds of illumination at 405 nm is sufficient to cleave PhoCl, removing the solubilization domain and enabling RGG-driven coacervation within minutes in cellular-sized water-in-oil emulsions. An optimized version of this system displayed light-induced coacervation in Saccharomyces cerevisiae. The methods described here provide novel strategies for inducing protein phase separation using light.

SUMMARY Protein clustering is pervasive in cell signaling, yet how signaling from higher-order assemblies differs from simpler forms of molecular organization is still poorly understood. We present an optogenetic approach to switch between oligomers and heterodimers with a single point mutation. We apply this system to study signaling from the kinase Zap70 and its substrate linker for activation of T cells (LAT), proteins that normally form membrane-localized condensates during T cell activation. We find that fibroblasts expressing synthetic Zap70:LAT clusters activate downstream signaling, whereas one-to-one heterodimers do not. We provide evidence that clusters harbor a positive feedback loop among Zap70, LAT, and Src-family kinases that binds phosphorylated LAT and further activates Zap70. Finally, we extend our optogenetic approach to the native T cell signaling context, where light-induced LAT clustering is sufficient to drive a calcium response. Our study reveals a specific signaling function for protein clusters and identifies a biochemical circuit that robustly senses protein oligomerization state., In brief Dine et al. study how different modes of molecular organization contribute to cell signaling using the kinase Zap70 and its substrate LAT as a model system. Optogenetic manipulation reveals that LAT:Zap70 clusters—but not dimers—trigger potent signaling via localized positive feedback among LAT, Zap70, and Src-family kinases., Graphical abstract

The modular synthesis of a library containing seven self-assembling amphiphilic Janus dendrimers is reported. Three of these molecules contain environmentally friendly chiral-racemic fluorinated dendrons in their hydrophobic part (RF), one contains achiral hydrogenated dendrons (RH), while one denoted hybrid Janus dendrimer, contains a combination of chiral-racemic fluorinated and achiral hydrogenated dendrons (RHF) in its hydrophobic part. Two Janus dendrimers contain either chiral-racemic fluorinated dendrons and a green fluorescent dye conjugated to its hydrophilic part (RF-NBD) or achiral hydrogenated and a red fluorescent dye in its hydrophilic part (RH-RhB). These RF, RH, and RHF Janus dendrimers self-assembled into unilamellar or onion-like soft vesicular dendrimersomes (DSs), with similar thicknesses to biological membranes by simple injection from ethanol solution into water or buffer. Since RF and RH dendrons are not miscible, RF-NBD and RH-RhB were employed to investigate by fluorescence microscopy the self-sorting and co-assembly of RF and RH as well as of phospholipids into hybrid DSs mediated by the hybrid hydrogenated-fluorinated RHF Janus dendrimer. The hybrid RHF Janus dendrimer co-assembled with both RF and RH. Three-component hybrid DSs containing RH, RF, and RHF were formed when the proportion of RHF was higher than 40%. With low concentration of RHF and in its absence, RH and RF self-sorted into individual RH or RF DSs. Phospholipids were also co-assembled with hybrid RHF Janus dendrimers. The simple synthesis and self-assembly of DSs and hybrid DSs, their similar thickness with biological membranes and their imaging by fluorescence and 19F-MRI make them important tools for synthetic biology.

Protein engineering enables the creation of materials with designer functionality and tailored responsiveness. Here, we design a protein with two control motifs for its phase separation into micron sized liquid droplets – one driven by a hydrophobic domain and the other by oxidation of a disulfide bond. Our work is based on the plant surfactant protein, oleosin, which has a hydrophobic domain but no cysteines. Oleosin phase separates to form liquid droplets below a critical temperature akin to many naturally occurring membrane-less organelles. Sequence mutations are made to introduce a cysteine residue into oleosin. The addition of a cysteine causes phase separation at a lower concentration and increases the phase transition temperature. Adding a reducing agent to phase-separated, cysteine-containing oleosin rapidly dissolves the droplets. The transition temperature can be tuned by varying the location of the cysteine or by blending the parent cysteine-less molecule with the cysteine containing mutant. This provides a novel way to control protein droplet formation and dissolution. We envision this work having applications as a system for the release of a protein or drug with engineered sensitivity to reducing conditions and as a mimic of membrane-less organelles in synthetic protocells.

Polymersomes are robust vesicles made from amphiphilic block co-polymers. Large populations of uniform giant polymersomes with defined, entrapped species can be made by templating of double-emulsions using microfluidics. In the present study, a series of two enzymatic reactions, one inside and the other outside of a polymersome, were designed to give rise to induced rupture of polymersomes. We measured how the kinetics of rupture were affected by altering enzyme concentration. These results suggest that protocells with entrapped enzymes can be engineered to secrete entrapped materials on cue.

We detail the influence of tapered interfaces on the nanoscale morphologies of ion-doped poly(styrene-b-oligo-oxyethylene methacrylate) block polymers (BPs). Most significantly, the location of double-gyroid network phase window was found in ion-doped normal-tapered materials, and a similar window was not detectable in the corresponding non-tapered and inverse-tapered BPs. Additionally, the effective interaction parameters, χeff, were reduced substantially in the tapered materials in comparison with their non-tapered counterparts. Overall, this work demonstrates that tapering between polymer blocks provides unique control over BP morphologies and improves the material processability (due to lower χeff), potentially facilitating the development of future ion-conducting devices.

Significance Cells are decorated with charged and uncharged carbohydrate ligands known as glycans, which are responsible for several key functions, including their interactions with proteins known as lectins. Here, a platform consisting of synthetic nanoscale vesicles, known as glycodendrimersomes, which can be programmed with cell surface-like structural and topological complexity, is employed to dissect design aspects of glycan presentation, with specificity for lectin-mediated bridging. Aggregation assays reveal the extent of cross-linking of these biomimetic nanoscale vesicles—presenting both anionic and neutral ligands in a bioactive manner—with disease-related human and other galectins, thus offering the possibility of unraveling the nature of these fundamental interactions., Precise translation of glycan-encoded information into cellular activity depends critically on highly specific functional pairing between glycans and their human lectin counter receptors. Sulfoglycolipids, such as sulfatides, are important glycolipid components of the biological membranes found in the nervous and immune systems. The optimal molecular and spatial design aspects of sulfated and nonsulfated glycans with high specificity for lectin-mediated bridging are unknown. To elucidate how different molecular and spatial aspects combine to ensure the high specificity of lectin-mediated bridging, a bottom-up toolbox is devised. To this end, negatively surface-charged glycodendrimersomes (GDSs), of different nanoscale dimensions, containing sulfo-lactose groups are self-assembled in buffer from a synthetic sulfatide mimic: Janus glycodendrimer (JGD) containing a 3′-O-sulfo-lactose headgroup. Also prepared for comparative analysis are GDSs with nonsulfated lactose, a common epitope of human membranes. These self-assembled GDSs are employed in aggregation assays with 15 galectins, comprising disease-related human galectins, and other natural and engineered variants from four families, having homodimeric, heterodimeric, and chimera architectures. There are pronounced differences in aggregation capacity between human homodimeric and heterodimeric galectins, and also with respect to their responsiveness to the charge of carbohydrate-derived ligand. Assays reveal strong differential impact of ligand surface charge and density, as well as lectin concentration and structure, on the extent of surface cross-linking. These findings demonstrate how synthetic JGD-headgroup tailoring teamed with protein engineering and network assays can help explain how molecular matchmaking operates in the cellular context of glycan and lectin complexity.

A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated–fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare submicron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.

Paradigm-shifting research has revealed that certain intrinsically disordered proteins (IDPs) phase separate into spherical liquid droplets that act as membrane-less organelles in living cells. Here, we investigated protease activity as a strategy for triggering controlled droplet disassembly without changing temperature, salt concentration, or other variables that are difficult to manipulate in vivo. We selected a naturally occurring phase-separating IDP, the RGG domain from LAF-1, and produced a variant consisting of two RGG domains in tandem. This RGG tandem protein exhibits enhanced phase behavior - that is, it self-assembles into liquid droplets at lower protein concentration and higher temperature as compared to a single RGG domain. We incorporated a thrombin cleavage site between the two RGG domains of this construct and discovered that upon treatment of the RGG tandem droplets with thrombin, the droplet diameter shrank at a rate of 0.5 micrometers per hour, as measured by quantitative optical microscopy. This occurred because the single RGG domains that result upon cleavage of RGG tandem with thrombin have weaker phase behavior and do not phase separate under the same conditions as does RGG tandem. Through additional protein engineering, we generated a variant that releases a fluorescent reporter when the protein droplet disassembles upon treatment with protease. This is a modular platform for enzymatically-triggered disassembly and release of proteins from droplets. We envision applications of this concept in protein drug delivery, such as in release of antimicrobial peptides for wound healing, and in controlling the behavior of membrane-less organelles within cells in an inducible manner.