Lian He

The nucleolus is a subnuclear membraneless compartment intimately involved in ribosomal RNA synthesis, ribosome biogenesis and stress response. Multiple optogenetic devices have been developed to manipulate nuclear protein import and export, but molecular tools tailored for remote control over selective targeting or partitioning of cargo proteins into subnuclear compartments capable of phase separation are still limited. Here, we report a set of single-component photoinducible nucleolus-targeting tools, designated pNUTs, to enable rapid and reversible nucleoplasm-to-nucleolus shuttling, with the half-lives ranging from milliseconds to minutes. pNUTs allow both global protein infiltration into nucleoli and local delivery of cargoes into the outermost layer of the nucleolus, the granular component. When coupled with the amyotrophic lateral sclerosis (ALS)-associated C9ORF72 proline/arginine-rich dipeptide repeats, pNUTs allow us to photomanipulate poly-proline–arginine nucleolar localization, perturb nucleolar protein nucleophosmin 1 and suppress nascent protein synthesis. pNUTs thus expand the optogenetic toolbox by permitting light-controllable interrogation of nucleolar functions and precise induction of ALS-associated toxicity in cellular models.

As two prominent examples of intracellular single‐domain antibodies or antibody mimetics derived from synthetic protein scaffolds, monobodies and nanobodies are gaining wide applications in cell biology, structural biology, synthetic immunology, and theranostics. Herein, a generally applicable method to engineer light‐controllable monobodies and nanobodies, designated as moonbody and sunbody, respectively, is introduced. These engineered antibody‐like modular domains enable rapid and reversible antibody–antigen recognition by utilizing light. By the paralleled insertion of two light‐oxygen‐voltage domain 2 modules into a single sunbody and the use of bivalent sunbodies, the range of dynamic changes of photoswitchable sunbodies is substantially enhanced. Furthermore, the use of moonbodies or sunbodies to precisely control protein degradation, gene transcription, and base editing by harnessing the power of light is demonstrated.

In article number 2002148, Yubin Zhou, Guolin Ma, Yun Huang, and co‐workers developed a caffeine‐operated synthetic module (COSMO), a potent chemically‐induced dimerization system that can be switched on by caffeine and its metabolites, as well as caffeinated beverages and chocolates consumed in our daily life. COSMO enables caffeine‐inducible gating of calcium channels, activation of cell signaling, tumor cell killing via necroptosis, and enhancement of viral antigen recognition for the SARS‐CoV‐2 spike protein.

The spatiotemporal organization of oligomeric protein complexes and translocons, such as the supramolecular organizing centers (SMOC) made of MyDDosome and MAVSome, are essential for transcriptional activation of host inflammatory responses and immune metabolisms. Light-inducible assembly of MyDDosome and MAVSome are presented herein to induce activation of nuclear factor-kB (NF-κB) and type-I interferons (IFNs). Engineering of SMOCs and the downstream transcription factor permits programmable and customized innate immune operations in a light-dependent manner. These synthetic molecular tools will likely enable optical and user-defined modulation of innate immunity at a high spatiotemporal resolution to facilitate mechanistic studies of distinct modes of innate immune activations and potential intervention of immune disorders and cancer.

Autophagy is an intracellular recycling process that maintains cellular homeostasis by orchestrating immunity upon viral infection. Following viral infection, autophagy is often initiated to curtail infection by delivering viral particles for lysosomal degradation and further integrating with innate pattern recognition receptor signaling to induce interferon (IFN)-mediated viral clearance. However, some viruses have evolved anti-autophagy strategies to escape host immunity and to promote viral replication. In this chapter, we illustrate how autophagy prevents viral infection to generate an optimal anti-viral milieu, and then concentrate on how viruses subvert and hijack the autophagic process to evade immunosurveillance, thereby facilitating viral replication and pathogenesis. Understanding the interplays between autophagy and viral infection is anticipated to guide the development of effective anti-viral therapeutics to fight against infectious diseases.

Autophagy is an intracellular degradation and recycling machinery by which cellular materials are delivered to the lysosome for disposal. Beyond lysosomal degradation, autophagy genes play additional roles in secretion and membrane-trafficking pathways. Ranging from cell-intrinsic and cell-type-specific regulation of innate inflammatory signaling pathways to intercellular cross talk through secretion of soluble factors (e.g., shaping the MHC immunopeptidome for T cell response, etc.), autophagy exerts multiple functions in driving inflammation and modulating the pathological progression of immune-related disorders such as neurodegenerative diseases, inflammatory bowel diseases, autoimmunity, and metabolic diseases. Notably, owing to the complexity of autophagy process involving multiple proteins and stepwise assembly of protein complexes, noncanonical forms of autophagy or autophagic proteins, which function beyond autophagy, are equally important in the maintenance of cellular homeostasis and pathogenesis. This chapter summarizes the most up-to-date findings of autophagy proteins in the regulation of immune-related diseases. Understanding of the autophagy machinery offers therapeutic strategies for treating inflammatory diseases.