Proximity labeling rests on a deceptively simple idea. Instead of trying to capture fragile or transient interactions directly, researchers fuse an engineered enzyme to a molecule of interest and let that enzyme chemically tag everything nearby. The tagged neighbors can then be purified and identified by mass spectrometry or sequencing, producing a snapshot of the local molecular environment. Enzymes such as APEX2, which uses hydrogen peroxide to drive radical generation, and TurboID, an evolved derivative of biotin ligase, have transformed the study of protein complexes and organelle proteomes. Applying the same logic to RNA, however, has proven far more difficult, because RNA molecules are chemically distinct, often abundant, and embedded in ribonucleoprotein assemblies that are easily disrupted by harsh labeling conditions.

Lantern was developed to address precisely this gap. The enzyme is designed to label molecules in the immediate vicinity of a chosen RNA, generating a record of the proteins and other RNAs that associate with it in living cells. Early versions of the tool, like many first-generation proximity labeling systems, faced limitations in catalytic rate, background activity, and the conditions required to drive the labeling reaction. Slow enzymes require long labeling periods, during which the cell continues to change, blurring the temporal resolution of the resulting map. High background activity, meanwhile, can swamp genuine neighbors in a haze of nonspecific tags, obscuring the very interactions researchers hope to detect.

Directed evolution offers a systematic way out of this impasse. The approach mimics natural selection in the laboratory: researchers generate large libraries of enzyme variants carrying random mutations, screen or select the variants that perform best on a defined task, and then iterate the process, accumulating beneficial mutations over successive rounds. Applied to Lantern, this strategy allowed the team to interrogate enormous sequence space and identify combinations of mutations that jointly improved catalytic turnover, reduced background, and preserved the enzyme’s ability to function inside the complex chemical environment of a mammalian cell. The result is an evolved Lantern variant that labels proximal RNA and protein molecules far more rapidly than its predecessors.

The significance of speed in proximity labeling is difficult to overstate. Cellular states are not static; signaling events, stress responses, and cell-cycle transitions can remodel the interactome of an RNA within minutes. A labeling reaction that requires hours effectively averages over all of these changes, producing a composite picture that may not correspond to any real biological moment. A fast enzyme, by contrast, can capture a molecular neighborhood on a timescale that approaches the dynamics of the underlying biology. This temporal precision matters enormously for studying processes such as RNA granule assembly, stress granule formation, and the rapid redistribution of RNAs during cellular responses to external stimuli.

Dual labeling of both RNA and protein by the same enzyme is another defining feature of the evolved Lantern system. Most existing tools are specialized: some tag proteins efficiently but leave RNA untouched, while RNA-targeting approaches often rely on separate chemistries that are difficult to reconcile in a single experiment. A unified catalyst that marks both classes of molecules in the vicinity of a target simplifies experimental design and enables genuinely integrated maps of ribonucleoprotein architecture. Because RNA-binding proteins and their RNA partners form tightly interwoven networks, the ability to profile both sides of the interface from a single labeling event provides a more complete and internally consistent picture than combining results from separate, independently optimized systems.

The technical challenges that directed evolution had to overcome are worth appreciating in detail. An ideal proximity labeling enzyme must remain inactive until deliberately deployed, tolerate fusion to diverse RNA-targeting modules such as Cas proteins or RNA-binding domains, operate at physiological temperature and pH, and generate reactive intermediates that diffuse only over a short range before reacting with nearby molecules. Balancing these competing demands is not intuitive; mutations that boost catalytic activity often increase background or alter substrate specificity in undesirable ways. Screening strategies that evaluate variants directly in cellular contexts, rather than in simplified biochemical assays, are therefore essential for identifying enzymes that perform well where it matters, inside living cells rather than in a test tube.

Beyond its immediate technical achievements, the evolved Lantern system points toward broader applications across biology and medicine. Mapping the protein companions of disease-associated noncoding RNAs could reveal how long noncoding RNAs execute their regulatory functions and how mutations disrupt these interactions in conditions ranging from cancer to neurodegeneration. Viral RNAs, which recruit host factors into specialized replication and packaging complexes, could be profiled with unprecedented temporal resolution, illuminating points of vulnerability for antiviral therapeutics. In developmental biology, tracking the changing molecular neighborhoods of specific transcripts as cells differentiate could clarify how post-transcriptional regulation shapes cell fate decisions. The combination of speed, dual specificity, and genetic encodability makes the tool adaptable to virtually any RNA that can be targeted with a suitable binding module.

The study also contributes to a growing appreciation of directed evolution as an engine of innovation in chemical biology. Time and again, natural enzymes have proven to be starting points rather than finished solutions, and laboratory evolution has repeatedly delivered variants with properties that no rational design effort could have predicted. The Lantern work exemplifies this pattern: by letting mutation and selection explore sequence space under experimentally defined pressures, researchers obtained a catalyst whose performance characteristics reflect the specific demands of proximity labeling in living cells. As screening technologies improve and libraries grow larger and more diverse, the pace at which such optimized tools emerge is likely to accelerate, equipping the community with an ever-richer toolkit for interrogating molecular proximity.

For the field of RNA biology in particular, the arrival of a rapid, dual-function proximity labeling enzyme marks a meaningful step forward. The interactomes of RNAs have long been studied through laborious biochemical purification methods that require large quantities of material and inevitably perturb the very assemblies under investigation. A genetically encodable, fast-acting labeling system brings the study of RNA neighborhoods into the same experimental regime that has already revolutionized protein interaction mapping, with all the advantages of sensitivity, scalability, and compatibility with living systems. As researchers begin to apply evolved Lantern to their own questions, the coming years are likely to see a substantial expansion in our understanding of the molecular ecosystems that surround RNA, and of the roles those ecosystems play in health and disease.

Subject of Research: Directed evolution of the Lantern enzyme for rapid proximity labeling of RNA and proteins in living cells

Article Title: Directed evolution of Lantern enables rapid RNA and protein proximity labeling

Article References: Fang, Y., Ren, Z., Zheng, F., Wang, R., Zhao, S., Zhang, Y., Wang, W., Li, C., Liu-Yang, L., Lin, C., Liu, J., & Zou, P. (2026). Directed evolution of Lantern enables rapid RNA and protein proximity labeling. Nature Chemical Biology. https://doi.org/10.1038/s41589-026-02313-y

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02313-y

Keywords: directed evolution, Lantern, proximity labeling, RNA biology, protein labeling, RNA-protein interactions, chemical biology, ribonucleoprotein complexes, enzyme engineering, molecular interactome, living cells, Nature Chemical Biology

Cell engineering has become one of the most promising frontiers in biomedicine, underpinning therapies ranging from CAR-T cancer treatments to engineered probiotics. Yet the dominant tool for endowing cells with new abilities—genetic manipulation—carries inherent constraints. Editing multiple genes simultaneously is technically complex, and the tools that work in one species often fail to translate to another. As a result, building cells with sophisticated, multi-part functionalities through genetic means remains slow, costly and sometimes infeasible.

The cell surface offers a compelling alternative target. Because it mediates virtually every interaction a cell has with its environment, the surface is where therapeutic behavior can be most directly tuned. Surface biomolecules present a rich array of functional groups—amines, thiols and other reactive chemistry—that serve as natural anchoring points for chemical modification. Wang and Liu exploited this chemical accessibility by harnessing dopamine, a small molecule that self-polymerizes under mild, alkaline conditions into polydopamine, a adhesive layer first described in a landmark 2007 Science paper on mussel-inspired surface chemistry.

The beauty of the method lies in its simplicity and universality. When dopamine is added to a suspension of living bacteria under the right conditions, it polymerizes directly on the cell surface, forming a thin reactive coating that can simultaneously capture a second component of choice. In the protocol’s first procedure, that component is polyethylene glycol, or PEG, a hydrophilic polymer long known to help nanoparticles slip through mucus. The result is a PEGylated bacterium capable of penetrating the intestinal mucus layer and reinforcing the mucosal barrier—a potential preventive strategy against colitis. Excluding bacterial culture, preparing these mucus-penetrating bacteria takes roughly three hours.

The second procedure goes a step further with dual-functionalization. Here, polydopamine serves as the bridge between two distinct bioactive molecules on a single bacterium: an anti-PD1 antibody, a celebrated immune checkpoint inhibitor, and the S1 subunit of the SARS-CoV-2 spike protein, a viral antigen. The resulting synergy-immunoactivation bacteria are designed to simultaneously provoke anticancer immunity and antiviral immunity, offering a two-in-one platform for treating tumors while guarding against infection. This dual-functionalization procedure requires only about one hour of hands-on preparation time beyond bacterial culture.

Compared with conventional genetic manipulation and existing physicochemical surface modification techniques, the protocol’s versatility stands out. The polydopamine intermediate accepts both natural biological macromolecules, such as proteins and antibodies, and synthetic materials, and it tolerates the attachment of multiple diverse components in sequence. Because the chemistry does not depend on species-specific genetic machinery, it can in principle be applied to a wide range of cell types, from probiotic Escherichia coli Nissle 1917 to potentially other living cells, making it a genuinely cross-species platform.

The scientific foundations of the work draw on more than a decade of polydopamine research. Catecholic chemistry, first systematized for surface modification by Messersmith, Lee and colleagues, has been applied to countless materials, but extending it to living cells required careful optimization to ensure the polymerization conditions do not compromise cell viability. The Wang and Liu groups had previously demonstrated polymerization-mediated multifunctionalization of living cells in Advanced Materials in 2021, and their primary research papers—published in Nature Biomedical Engineering in 2024 on mucus-penetrating PEGylated bacteria and in Advanced Materials in 2023 on hybrid immunoactive nanosurface bacteria—provide the proof-of-concept data that underpin this protocol.

The therapeutic implications are substantial. For inflammatory bowel disease, the mucus-penetrating bacteria represent a novel way to shore up a failing intestinal barrier rather than simply delivering drugs. For oncology, bacteria coated with checkpoint inhibitors concentrate immunotherapy at tumor sites, potentially reducing the systemic toxicity associated with injected antibodies while leveraging the natural tumor-homing behavior of certain bacterial strains. And because the coating chemistry is modular, the same scaffold could in principle carry different antigen–antibody pairs to address other cancers or emerging viral threats.

The authors also confront the practical challenges facing any live biotherapeutic. Regulatory frameworks for live biotherapeutic products, as outlined by the US Food and Drug Administration, demand rigorous characterization of manufacturing and control, and a surface-engineered bacterium must demonstrate stability, safety and reproducibility at every step. The protocol addresses these concerns by providing detailed characterization procedures, including assessments of coating thickness, surface composition, bacterial viability, mucus penetration, and the immunogenicity and intratumoral distribution of the dual-functionalized bacteria. Jinyao Liu has additionally filed a patent related to the technology, signaling commercial interest alongside the academic contribution.

By transforming cell surface engineering from a specialized genetic exercise into an accessible chemical operation, the protocol lowers the barrier to entry for laboratories seeking to develop next-generation living therapeutics. The authors anticipate that the platform will offer valuable guidance for engineering living cells with designable, tailorable functionalities for innovative cell-based therapy. If the approach translates from the bench to the clinic as hoped, the humble chemistry of mussel glue may soon help dress living cells for battle against some of medicine’s most stubborn diseases.

Subject of Research: Dopamine polymerization-mediated chemical surface functionalization of living cells for cell-based therapy

Article Title: Dopamine polymerization-mediated surface functionalization of living cells for advanced therapeutic applications

Article References: Dopamine polymerization-mediated surface functionalization of living cells for advanced therapeutic applications. (n.d.). https://doi.org/10.1038/s41596-026-01422-1

Image Credits: AI Generated

DOI: 10.1038/s41596-026-01422-1

Keywords: dopamine polymerization, polydopamine, surface functionalization, living cells, bacterial therapeutics, mucus-penetrating bacteria, PEGylation, immune checkpoint inhibitor, anticancer immunity, antiviral immunity, cell engineering, colitis