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

The study, published in Nature Chemical Biology, describes a systematic pipeline in which human cells were treated with a library of small molecules while perturbing a broad panel of genes known to participate in genome maintenance. Each combination produced a measurable fitness signature—a fingerprint of viability, growth, and survival under stress. When those fingerprints were arranged into network form, they resolved into a chemogenomic map: a topological landscape in which drugs with similar mechanisms cluster together, and in which genes with related functions occupy neighboring positions. Such maps have proven their worth in cancer pharmacology before, where they revealed drug targets and resistance pathways that no one could have predicted from single-gene studies alone.

What makes the new analysis distinctive is its focus on the DNA damage response, the elaborate signaling network that detects broken strands of DNA, halts the cell cycle, coordinates repair machinery, and decides whether a damaged cell should live or die. Because so many cancer therapies—radiation, platinum drugs, topoisomerase inhibitors, PARP inhibitors—work by inflicting DNA damage, understanding the vulnerabilities and redundancies of this network is not an abstract scientific goal. It is a question that directly shapes treatment outcomes for millions of patients.

As the team clustered the chemical profiles, one signal kept surfacing. Compounds that disturb iron homeostasis—iron chelators that sequester the metal, and agents that expand the labile iron pool inside cells—produced genetic interaction patterns strikingly similar to compounds known to generate oxidative DNA damage. That convergence pointed to a mechanistic link: iron, through its well-documented role in Fenton chemistry, converts ordinary peroxide into hydroxyl radicals, the most destructive of the reactive oxygen species. Hydroxyl radicals attack DNA indiscriminately, producing strand breaks and oxidized bases that tax the same repair pathways mobilized by radiation and chemotherapy.

The linchpin of that link turned out to be peroxiredoxin 1, or PRDX1, a highly abundant enzyme whose canonical job is to detoxify peroxides inside the cell. Chemogenomic analysis showed that when PRDX1 function was compromised, cells became exquisitely sensitive to perturbations of iron metabolism. The map essentially revealed a dependency: iron-driven oxidative chemistry creates a peroxide burden, and PRDX1 is the gatekeeper that keeps that burden from escalating into lethal DNA damage. In cells with intact PRDX1, fluctuations in iron levels were tolerable; in cells lacking it, the same fluctuations translated into accumulating genome injury.

That discovery reframes PRDX1 from a general antioxidant housekeeper into a specific node of the DNA damage response. The enzyme, a member of the peroxiredoxin family of cysteine-based peroxidases, cycles between oxidized and reduced states as it destroys peroxide substrates. Its abundance in the nucleus and cytosol has long puzzled researchers—why does a cell need so much of it? The chemogenomic data suggest an answer in the language of vulnerability: PRDX1 provides the protective margin that allows cells to tolerate the continuous, low-level oxidative chemistry that accompanies normal metabolism, and that margin becomes decisive when DNA damage pushes iron-dependent radical production upward.

The iron-damage axis also has a darker face. In recent years, the cell biology community has converged on ferroptosis, a form of regulated cell death driven by iron-catalyzed lipid peroxidation, as a process with intimate ties to genome stress. The new map does not simply confirm that connection; it locates it within the broader architecture of the DNA damage response, showing that the same network that activates ATM and ATR kinases, deploys BRCA proteins, and summons the homologous recombination machinery is functionally coupled to peroxide metabolism and iron availability. Damage sensing and redox sensing, the map implies, are not separate systems but interlocking ones.

For oncology, the implications are immediately tantalizing. Many tumor types accumulate excess iron and rely heavily on antioxidant systems to survive their own metabolic output—a combination that makes them theoretically vulnerable to any therapy that removes their peroxide defense. If PRDX1 occupies that protective position in the iron-damage axis, then inhibiting it in an iron-rich tumor could tip the balance toward catastrophic, irreparable genome damage. Conversely, normal cells with lower labile iron loads might tolerate a PRDX1 inhibitor far better, creating the kind of therapeutic window that targeted therapy developers dream about. The chemogenomic framework makes such hypotheses testable at scale: rather than asking whether a single drug kills a single cell line, researchers can now ask where any new agent falls within the network of known damage-response dependencies.

The methodology itself deserves attention as a template. Chemogenomic mapping has matured into a discipline where perturbation libraries, high-content fitness assays, and computational embedding of interaction profiles generate maps with genuine predictive power. In this study, the authors systematically cross-referenced compound sensitivity profiles with gene perturbation data, using network inference to identify edges that classical pairwise screens would have missed. The PRDX1–iron connection is a proof of concept that such maps can surface biology that sits outside the conventional textbook divisions of the field—redox biochemistry emerging from a screen nominally designed to probe DNA repair.

There are, of course, caveats. Chemogenomic interactions describe statistical dependencies, and translating them into molecular mechanisms requires direct biochemical validation: measuring hydroxide radical generation, quantifying PRDX1 oxidation states during the damage response, and testing whether iron manipulation truly sensitizes PRDX1-deficient cells through the accumulation of double-strand breaks. The interaction maps are a hypothesis-generating engine, not a substitute for mechanism. But the strength of the approach lies precisely in its breadth—it surveys the whole terrain before anyone commits to digging a single hole, and it does so in a human cell context directly relevant to disease.

What emerges is a changed mental picture of genome maintenance. The DNA damage response has traditionally been drawn as a signaling diagram: kinases, adaptors, repair factors, and checkpoints connected by activation arrows. The chemogenomic map adds a chemical dimension to that diagram, weaving in iron pools, peroxide fluxes, and peroxidase capacity. A cell’s ability to survive a DNA break, in this view, depends not only on how fast it can find and repair the lesion but also on how well its redox buffers can contain the oxidative fallout that follows. PRDX1, sitting at the junction of those two requirements, now looks less like a background antioxidant and more like a strategic asset in the cell’s genome defense—raising the question of whether the next generation of cancer therapies will deliberately target the iron-damage axis to finish off tumors that have already been weakened by standard DNA-damaging treatment.

Subject of Research: A chemogenomic interaction map identifying a PRDX1-dependent axis linking iron metabolism and oxidative damage in the DNA damage response.

Article Title: Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response

Article References: O’Loughlin, T. A., Arab, A., Misiukiewicz, S., Montesano, E., Yogodzinski, C., Borah, A. A., Quarantotti, V., Lou, K., Rosen, B. S., Corn, J. E., Gianni, D., Kabir, S., Forment, J. V., & Gilbert, L. A. (2026). Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response. Nature Chemical Biology. https://doi.org/10.1038/s41589-026-02312-z

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02312-z

Keywords: chemogenomics, DNA damage response, PRDX1, peroxiredoxin 1, iron metabolism, ferroptosis, reactive oxygen species, Fenton chemistry, genome maintenance, cancer therapy, redox biology, Nature Chemical Biology

The conceptual foundation of the study rests on a tension that immunologists have wrestled with for decades. The classical view of phagocytosis describes a one-way road: a target particle is recognized by receptors on the macrophage membrane, enveloped by actin-driven membrane extension, sealed inside an intracellular vesicle called a phagosome, and then progressively acidified and enzymatically degraded as the phagosome matures through fusion with lysosomes. Under this model, anything the macrophage eats is destined for the degradative pathway. Peptides derived from digested proteins are loaded onto major histocompatibility complex molecules and presented to lymphocytes, closing the loop between innate scavenging and adaptive surveillance. The new work suggests that this pathway is not the only fate available to captured material, and that functional protein transfer to the plasma membrane competes with degradation during uptake.

Technically, the distinction between internalization and surface transfer is not trivial to demonstrate, because material that remains attached to the outside of a cell can masquerade as internalized cargo in conventional flow cytometry and bulk fluorescence assays. Experiments of this kind therefore depend on approaches that spatially resolve the membrane. The study’s conclusions hinge on the ability to distinguish proteins that have genuinely been routed to the macrophage surface from those merely riding on incompletely internalized particles or trapped in membrane ruffles. Proteins delivered to the surface in a functional state must retain at least some of their biochemical activity, a criterion that separates this phenomenon from passive adsorption of denatured fragments. The authors’ characterization of functionally active proteins appearing on the macrophage membrane after uptake thus implies a controlled trafficking event rather than an artifact of sample handling.

One implication of the finding concerns the growing appreciation of trogocytosis, the process by which cells exchange fragments of their plasma membrane and surface molecules through contact. Trogocytosis has been documented most extensively among lymphocytes and antigen-presenting cells, where a cell can literally strip membrane-associated ligands from a partner and wear them on its own surface. The macrophage behavior described in the new study can be understood as a related but distinct phenomenon: rather than acquiring proteins from another cell through direct intermembrane contact during a competitive interaction, the macrophage appears to reroute a portion of the cargo it engulfs back to its own membrane during the uptake process itself. The phrase live-cell uptake in the study’s title is significant, because it indicates that this transfer occurs when the macrophage consumes material from living cells, situations in which the membrane chemistry of the target and the dynamics of receptor engagement differ substantially from uptake of dead cells or inert particles.

The biochemical questions raised by the work are considerable. For a protein to appear on the external face of the macrophage plasma membrane in a functional form, it must traverse or bypass several membrane barriers. Cargo internalized by phagocytosis is enclosed within a vesicle whose lumen is topologically extracellular, which means that, in principle, a protein could reach the cell surface by fusion of recycling vesicles with the plasma membrane without ever entering the cytosol. This recycling route is well established for receptors that are internalized and returned to the surface, and the new study suggests that at least some captured functional proteins can piggyback on analogous recycling traffic. Alternatively, transfer could involve direct membrane continuity between the forming phagosome and the plasma membrane, or regurgitation of incompletely sealed uptake structures. Distinguishing among these routes is a central challenge for follow-up work.

Functional display of captured proteins could have far-reaching consequences for immune regulation. A macrophage that presents an active, intact protein on its surface is not merely advertising peptides for T cell inspection; it is offering other cells the opportunity to bind that protein, respond to its enzymatic activity, engage it as a ligand, or be inhibited by it. If the transferred proteins include, for example, receptors, adhesion molecules, complement regulators, or signaling ligands derived from the cells the macrophage has consumed, the macrophage could effectively adopt surface properties of its prey. Such molecular mimicry at the single-cell level would provide a mechanism by which tissue-resident macrophages continually update their surface identity to reflect the local environment they patrol, blurring the boundary between self-display and scavenged display.

The finding also speaks to long-standing puzzles in the biology of macrophage interactions with living cells. Macrophages routinely sample healthy cells through brief contacts and transient uptake events without triggering inflammation, a process that depends on the balance of activating and inhibitory signals received through receptors such as those in the signal regulatory protein and integrin families. If live-cell uptake can leave functional proteins on the macrophage surface, then even a fleeting phagocytic event could durably alter the macrophage’s signaling landscape. Proteins acquired from a healthy cell might include inhibitory ligands that reinforce tolerance, whereas proteins acquired from a stressed or transformed cell might advertise danger. In this way, surface protein transfer could convert every meal a macrophage takes into a change in its own phenotype, coupling immune surveillance at the level of tissues to reprogramming at the level of the single cell.

From the perspective of chemical biology, the study exemplifies a broader trend of interrogating immune phenomena with tools that track molecules rather than populations. Understanding that captured proteins can remain functional after transfer requires assays that measure activity, localization, and trafficking simultaneously, integrating live-cell imaging, biochemical fractionation of membrane compartments, and perturbation of vesicular transport pathways. The paper’s home in Nature Chemical Biology underscores this methodological character: the question is not only what the macrophage does, but how molecular movement between intracellular compartments and the plasma membrane can be resolved, quantified, and manipulated. Insights of this kind are likely to inform the design of drug delivery systems, because nanoparticles and antibody conjugates engineered for macrophage uptake may likewise find themselves displayed, intact and active, on the macrophage surface rather than sequestered internally.

Therapeutically, the implications span several domains. In cancer immunotherapy, macrophages infiltrating tumors are known to engulf tumor cells and tumor-derived material, and their subsequent behavior profoundly shapes the antitumor response. If live-cell uptake leaves functional tumor proteins on the macrophage surface, this could either help prime adaptive immunity by displaying intact targets for antibody binding, or subvert it by presenting tolerogenic ligands. In infectious disease, pathogens that manipulate phagocytosis might exploit the transfer pathway to decorate macrophages with their own surface molecules, a strategy that could aid immune evasion. In transplantation and autoimmunity, acquired display of donor- or self-derived functional proteins could tilt local immune signaling toward acceptance or attack. Each of these scenarios remains speculative pending direct evidence about which proteins are transferred and under what physiological conditions, but they illustrate why a shift in the fate map of phagocytosed material matters well beyond cell biology.

The study ultimately reframes the macrophage surface as an interface in constant negotiation with the cell’s dietary history. Rather than a fixed identity defined by genome-encoded receptor expression, the macrophage membrane emerges as a composite structure, continuously edited by the functional proteins the cell captures from its surroundings during live-cell uptake. Future work will need to identify the molecular machinery that directs captured proteins to the surface, determine the breadth of cargo that follows this route, establish how long acquired proteins persist and signal, and test whether the phenomenon operates in vivo across tissues and disease states. What the current finding establishes is that the degradative pipeline of phagocytosis has a branch point that earlier models did not anticipate, and that branch point places captured, functional proteins directly in the traffic of the immune system’s most voracious and influential scavenger cells.

Subject of Research: Protein transfer to the macrophage surface during live-cell phagocytic uptake

Article Title: Macrophages transfer functional proteins to their surface during live-cell uptake

Article References: Volk, R. F., Fan, A. C., Casebeer, S. W., Tejus, V. R., Condon, A. C., Zirak, B., Manon, N. A., Irkliyenko, I., Torralba, D. M., Tao, S., Pollini, T., Ramani, V., Maker, A. V., Krummel, M. F., Goodarzi, H., & Zaro, B. W. (2026). Macrophages transfer functional proteins to their surface during live-cell uptake. Nature Chemical Biology. https://doi.org/10.1038/s41589-026-02292-0

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02292-0

Keywords: macrophages, phagocytosis, live-cell uptake, protein transfer, cell surface display, trogocytosis, innate immunity, membrane trafficking, Nature Chemical Biology, immune regulation, phagosome recycling, chemical biology

The new work, published in Nature Chemical Biology, tackles a problem that has frustrated the apoptosis field since BAX was first implicated in ischemic injury: the protein is a moving target. In healthy cells, BAX lounges in the cytosol as an inactive monomer, its lethal membrane-penetrating helices tucked away inside its own structure. Only when death signals accumulate does BAX undergo a dramatic conformational transformation, exposing its N-terminus, unfurling its ninth alpha helix, and migrating to the mitochondrial outer membrane, where it oligomerizes into pores. Small molecules that bind the resting state have been described before, but they tend to be weak, poorly characterized, or reactive with many unrelated proteins, making them unreliable tools and even less reliable medicines.

The team behind the new study took a different approach: rather than hunting for a generic binder, they engineered a covalent warhead aimed at a specific cysteine residue on the surface of inactive BAX. Covalent inhibitors have enjoyed a renaissance in recent years, most famously in the form of acrylamide-based drugs that target a non-catalytic cysteine in EGFR-mutant lung cancer. The strategy offers the allure of prolonged target engagement at low drug concentrations, but it carries a well-known risk: off-target reactivity with the many cysteine-rich proteins floating in any cell. The challenge, therefore, was to design a ligand whose reactivity is only unleashed in the precise geometric context of the BAX binding pocket.

That is where the concept of enantioselectivity becomes central. Small drug-like molecules typically exist as two enantiomers, mirror-image forms that are chemically identical in an achiral test tube but profoundly different in the chiral environment of a living cell. Enzymes, receptors, and protein binding pockets distinguish between these mirror images with exquisite sensitivity, often binding one form tightly while ignoring the other. The researchers exploited this principle twice over: first by synthesizing both enantiomers of their candidate inhibitor and then by demonstrating that only one of them engages BAX efficiently, while the opposite enantiomer is essentially inert. This one-handed specificity is a hallmark of a well-behaved chemical probe and stands in sharp contrast to earlier BAX inhibitors whose activity could not be cleanly separated from nonspecific protein damage.

The design process began with structural analysis of the inactive BAX monomer, using prior nuclear magnetic resonance structures and molecular docking to identify a pocket adjacent to a reactive cysteine. The team then iterated through a series of analogues, tuning the electrophilic warhead and the surrounding scaffold until they achieved a compound that reacts with BAX rapidly and selectively in competition assays against a broad panel of cysteine-containing proteins. Chemoproteomic experiments in cell lysates confirmed the selectivity on a proteome-wide scale, showing that the compound’s covalent footprint is dominated by BAX rather than by the hundreds of other cysteine residues available for reaction. This kind of global reactivity profiling has become the gold standard for validating covalent chemistry, and its successful application here lends substantial credibility to the probe.

With a selective inhibitor in hand, the researchers turned to functional testing. In cell culture, the compound protected cells from apoptotic death provoked by a variety of stresses, and the protection was abolished when BAX was removed or when a non-reactive analogue was substituted, establishing that the cytoprotective effect runs through the intended target. Biochemical assays showed that the covalently modified BAX can no longer expose its membrane-inserting helix or translocate to mitochondria in response to activating signals, effectively locking the protein in its harmless resting conformation. The modification also prevented BAX oligomerization, the downstream step that converts individual protein molecules into the pore-forming assemblies that rupture the mitochondrial membrane and release cytochrome c.

The most consequential experiments, however, were performed in living animals. In a mouse model of ischemia-reperfusion injury, a scenario that mirrors the cellular damage that follows a heart attack or stroke, administration of the active enantiomer significantly reduced tissue damage compared with vehicle controls. Critically, the mirror-image enantiomer, which lacks BAX reactivity in vitro, provided no protection, a rigorous in vivo control that ties the therapeutic benefit directly to the covalent engagement of BAX. Pharmacokinetic measurements confirmed that the compound reaches relevant tissues at concentrations sufficient to modify the target, and the treated animals tolerated the drug without overt toxicity, an encouraging early signal for a strategy that modifies a protein involved in fundamental cellular quality control.

Experts in the apoptosis field have long debated whether inhibiting BAX systemically is safe or even desirable, given the protein’s role in eliminating damaged or potentially cancerous cells. The new study does not resolve that debate, but it sharpens the terms of the discussion. Because the inhibitor is covalent and long-acting, dosing regimens could in principle be tailored to acute, short-term scenarios, such as the hours surrounding reperfusion therapy after a myocardial infarction, where transient BAX inhibition might salvage tissue without the long-term cancer risks that chronic suppression might entail. The authors’ demonstration that a single enantiomer drives the entire pharmacological effect also suggests that medicinal chemistry optimization can proceed with confidence, since the inactive mirror image provides a built-in negative control for every future experiment.

The work also carries broader lessons for chemical biology. Covalent inhibitors were once viewed as liabilities to be engineered out of drug candidates; today they are a deliberate design choice, provided that selectivity is demonstrated rigorously. The BAX program illustrates the full pipeline: structural insight to identify a ligandable site, warhead tuning to balance reactivity and selectivity, enantiomer pairing to isolate specific from nonspecific effects, chemoproteomics to survey the proteome, and animal models to test whether the molecular mechanism translates into tissue-level protection. Each step reinforces the others, and the resulting probe is far more than a tool; it is a proof of concept that a notoriously difficult, conformationally dynamic protein can be drugged with precision.

Looking ahead, the researchers and their colleagues face the familiar gauntlet of translation: optimizing potency and pharmacokinetics, assessing safety across longer time horizons, and identifying the clinical settings where BAX inhibition offers the greatest benefit at the least risk. Beyond ischemic injury, candidates include neurodegenerative conditions in which mitochondrial apoptosis contributes to neuronal loss, and organ transplantation, where protecting donor tissue from programmed death could extend viability and improve outcomes. Whatever the ultimate therapeutic destination, the demonstration that an enantioselective covalent inhibitor of BAX can confer cytoprotection in vivo marks a milestone in the long campaign to control the machinery of cell death, and it hands the field a chemical instrument of unprecedented specificity for dissecting BAX biology in health and disease.

Subject of Research: Development of an enantioselective covalent small-molecule inhibitor of the pro-apoptotic protein BAX that prevents mitochondrial apoptosis and provides cytoprotection in vivo.

Article Title: An enantioselective covalent inhibitor of BAX confers cytoprotection in vivo

Article References: An enantioselective covalent inhibitor of BAX confers cytoprotection in vivo. (n.d.). https://doi.org/10.1038/s41589-026-02297-9

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02297-9

Keywords: BAX, apoptosis, covalent inhibitor, enantioselectivity, mitochondria, cytoprotection, ischemia-reperfusion injury, chemical biology, drug design, chemoproteomics, Nature Chemical Biology, cell death

Transfer RNA molecules are not naked RNA strands; they are heavily decorated with chemical groups that fine-tune their stability, folding, and ability to recognize codons on the ribosome. More than a hundred distinct modified nucleosides have been catalogued across the three domains of life, ranging from simple methyl groups to elaborate, multi-ring structures that require whole cascades of enzymes to assemble. Some of the most chemically ambitious modifications are found in bacteria, where they help organisms survive in hostile environments, tune translation in response to stress, and even contribute to antibiotic resistance. The aminovaleramide modification reported by the AvaS research joins this growing catalogue as a striking example of amide chemistry carried out directly on RNA.

Pyridoxal phosphate, commonly abbreviated PLP, is a cofactor with a legendary reputation in enzymology. It sits at the reactive heart of enzymes that make, break, and rearrange amino acids, enabling transformations that would otherwise demand harsh laboratory conditions. PLP achieves this by forming an internal aldimine, a Schiff base linkage, with a lysine residue in the enzyme’s active site. When an amino acid substrate arrives, the linkage is exchanged in a transamination step that produces an external aldimine, positioning the substrate for reactions ranging from decarboxylation to side-chain cleavage. What makes the AvaS discovery remarkable is that this canonical amino acid chemistry appears to have been recruited for RNA biosynthesis, in effect coupling amino acid metabolism to the chemical maturation of tRNA.

According to the study, AvaS catalyzes the formation of aminovaleramide through a PLP-dependent route that resembles pathways used to synthesize certain amino acid-derived metabolites. The reaction logic involves the cofactor-mediated processing of an amino acid precursor, likely through condensation and rearrangement steps that generate an activated intermediate, followed by transfer of the resulting aminovaleramide moiety onto the tRNA scaffold. This kind of cofactor-dependent construction on RNA is rare. Most known tRNA modification enzymes rely on S-adenosylmethionine for methyl and threonylcarbamoyl chemistry, or on ATP-driven activation reactions to ligate smaller groups onto nucleotides. A PLP enzyme acting on tRNA therefore represents a mechanistic surprise, suggesting that the boundary between primary metabolism and RNA modification biochemistry is more porous than previously appreciated.

The identification of AvaS also illustrates the power of modern bioinformatic screens. Rather than stumbling across the enzyme by chance, the researchers were able to trace the modification’s occurrence by following the distribution of gene clusters whose sequence features hinted at PLP-dependent chemistry linked to RNA processing. Genes encoding tRNA modification enzymes frequently cluster with partner genes, exporter proteins, or resistance determinants, a pattern known as neighboring gene logic. By scanning bacterial genomes for such clusters, and by asking which organisms contain both the predicted modification machinery and the chemical signature of aminovaleramide-containing nucleosides, the team narrowed the search to a manageable set of candidate enzymes and then validated their predictions experimentally.

Once AvaS was confirmed as the biosynthetic enzyme, the structural and mechanistic characterization proceeded along classical enzymological lines, with modern tools. Recombinant production of the protein allowed the researchers to test its activity in vitro, demonstrating that purified AvaS could carry out the key chemical steps without the rest of the cellular milieu. Mass spectrometry of digested nucleosides confirmed the identity of the aminovaleramide product, while comparisons with catalytic mutants and cofactor-free controls established that PLP is genuinely required, not merely tolerated. These experiments collectively argue that a single enzyme can perform a multi-step biosynthesis, assembling the modification before or during its attachment to RNA, rather than relying on a separate pathway to pre-build the transferable group.

Why would a bacterium invest energy in constructing such an elaborate modification? The most likely answers relate to translation fidelity and stress physiology. Modified bases near the anticodon loop of tRNA influence how reliably the molecule pairs with messenger RNA codons, and disruptions to these modifications typically cause ribosomal frameshifting, slowed growth, or heightened sensitivity to environmental challenges. Amide-bearing modifications can also alter the local geometry and hydrogen-bonding pattern of the tRNA in ways that stabilize particular conformations of the anticodon loop. In pathogenic or environmental bacteria, such fine-tuning can mean the difference between thriving and failing under thermal, oxidative, or nutrient stress, which in turn makes the underlying enzymes attractive subjects for study as potential antimicrobial targets.

The discovery carries implications beyond microbiology. RNA chemical biology has been undergoing a renaissance, driven partly by interest in modified nucleosides as biomarkers, as regulators of gene expression, and as engineering targets for synthetic biology. Finding that a cofactor as central as PLP participates directly in RNA modification suggests that other seemingly improbable chemistries may also be lurking in unexplored genomic corners. The aminovaleramide modification itself, featuring a terminal amino group on a five-carbon chain linked through an amide bond, is chemically rich, and understanding how enzymes build and install such groups could inspire new methods for site-specific RNA labeling or the design of modified oligonucleotide therapeutics.

There are also evolutionary questions raised by the work. PLP-dependent enzymes form large and ancient protein superfamilies, and the AvaS result adds a new functional branch to that family tree. Determining whether the RNA-modifying activity arose by divergence from an amino acid biosynthetic ancestor, or through convergent recruitment of PLP chemistry into an unrelated scaffold, will require broader phylogenetic analysis. The study’s genomic survey provides a starting point, mapping where AvaS homologs occur across bacterial phyla and hinting at horizontal gene transfer events that may have spread the capability between distantly related organisms. Such analyses often reveal that RNA modification systems evolve rapidly, shaped by the arms races between microbes, their viruses, and their chemical environments.

For the field of tRNA biology, the AvaS report is a reminder of how much chemical diversity remains undocumented. Decades of focused work on well-studied model organisms, such as Escherichia coli and Saccharomyces cerevisiae, produced detailed maps of their modification landscapes, but the vast majority of bacterial species have never been surveyed with modern nucleoside mass spectrometry. As high-throughput analytical methods and genome-mining approaches converge, enzymes like AvaS are expected to surface with increasing frequency, each one a potential new tool for manipulating RNA and a potential window into unexplored metabolic logic. The PLP-dependent construction of aminovaleramide stands as an early and vivid example of what that exploration is likely to yield.

Subject of Research: Pyridoxal phosphate-dependent biosynthesis of the tRNA modification aminovaleramide by the bacterial enzyme AvaS

Article Title: Pyridoxal-phosphate-dependent biosynthesis of aminovaleramide by AvaS in tRNA

Article References: Sun, J., Wu, J., Yuan, Y., Balamkundu, S., Dziergowska, A., Chay Suen Suen, H., Dwijapriya, Liang, C., Hardy, L., Lee, M. E., Leszczynska, G., Liu, C.-F., Baharoglu, Z., Drouard, L., Bruner, S. D., Begley, T. J., de Crécy-Lagard, V., & Dedon, P. C. (2026). Pyridoxal-phosphate-dependent biosynthesis of aminovaleramide by AvaS in tRNA. Nature Chemical Biology. https://doi.org/10.1038/s41589-026-02303-0

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02303-0

Keywords: tRNA modification, AvaS, pyridoxal phosphate, aminovaleramide, vitamin B6, enzyme mechanism, RNA chemical biology, bacterial genomes, translation fidelity, nucleoside mass spectrometry, bioinformatic gene mining, Nature Chemical Biology

Redox cofactors are the molecular batteries of the cell. They accept and donate electrons in the tightly choreographed reactions that underpin respiration, photosynthesis, biosynthesis and detoxification. The canonical cofactors—molecules such as flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP)—are so widespread that their presence in an enzyme active site is often assumed rather than demonstrated. But over the past several years, researchers have identified a series of modified and entirely distinct cofactors: prenylated flavins such as flavin adenine dinucleotide modified with a prenyl group, deazaflavins like F420, quinone-derived cofactors such as topaquinone and tryptophan tryptophylquinone, and metal-organic species that defy easy classification. These noncanonical cofactors enable chemistries that standard flavins and nicotinamides cannot easily achieve, including hydride transfers at unusual redox potentials, radical-mediated rearrangements and C–C bond formations that would be difficult with conventional catalysis.

The central puzzle addressed in the new work is one of recognition and assembly. If an enzyme uses a noncanonical cofactor, how does the protein know to bind that cofactor rather than its more abundant canonical cousin? And how can bioinformaticians predict, from sequence alone, which of the millions of uncharacterized proteins in genomic databases depend on these exotic helpers? The answer, according to the study, lies in a short, recurring sequence motif—a conserved stretch of amino acids that acts as a molecular postcode, directing the enzyme’s cofactor-binding pocket toward noncanonical chemistry.

Sequence motifs have long served as the workhorses of computational biology. Short conserved patterns, such as the P-loop that binds nucleotide phosphates or the zinc-finger motifs that coordinate metal ions in DNA-binding proteins, allow researchers to assign function to proteins that have never been isolated in a laboratory. The newly identified motif performs a similar role for redox cofactor selection. By scanning families of flavin-dependent enzymes and comparing those known to use standard FAD or FMN with the smaller subset confirmed to use modified or alternative cofactors, the researchers identified a conserved pattern of residues that appears with striking regularity in the noncanonical group and is conspicuously absent from the canonical one. Mutational experiments confirmed that altering these residues in a noncanonical enzyme abolished its ability to accommodate the alternative cofactor, while introducing the motif into a canonical scaffold shifted its cofactor preference—a result that establishes the motif as a genuine determinant of cofactor identity rather than a coincidental correlation.

The implications of this finding extend well beyond the specific enzyme families examined in the study. Genomic surveys suggest that proteins carrying the motif are distributed across a remarkable range of organisms, from soil-dwelling actinobacteria—long recognized as prolific producers of bioactive natural products—to human-associated microbes and even some archaeal lineages. In many of these organisms, the motif-bearing enzymes cluster within biosynthetic gene clusters, the compact genomic neighborhoods that encode the assembly lines for antibiotics, antitumor agents and other specialized metabolites. This genomic context hints at a widespread and previously underappreciated role for noncanonical redox chemistry in natural product biosynthesis, suggesting that many of the structurally exotic metabolites isolated from microbes over the past half-century may owe their existence to enzymes quietly using cofactors that standard annotation pipelines would never flag.

One of the most exciting consequences of the work is predictive. Armed with the motif, researchers can now interrogate sequence databases with a simple pattern search and retrieve a curated list of candidate enzymes likely to use noncanonical cofactors. This transforms what has historically been a slow, serendipitous process—discover a strange metabolite, purify the enzyme responsible, and only then realize the cofactor is unusual—into a rational, hypothesis-driven workflow. Biochemistry can then be targeted at the most promising candidates, prioritizing enzymes from gene clusters associated with medicinally relevant compound classes. In an era when the rate of genome sequencing vastly outpaces the rate of experimental characterization, tools that convert sequence information into functional predictions are among the most valuable commodities in the life sciences.

The discovery also carries significant weight for synthetic biology and enzyme engineering. Noncanonical cofactors often possess redox potentials and reactivity profiles that canonical cofactors cannot match. F420, for example, the deazaflavin cofactor best known from methanogenic archaea, mediates hydride transfer reactions at potentials inaccessible to NAD and NADP, and engineered F420-dependent enzymes have already been explored for the degradation of persistent pollutants and the production of pharmaceutical intermediates. Prenylated flavins, meanwhile, catalyze photochemical reactions that ordinary flavins cannot, and their light-driven chemistry is being harnessed in optogenetic tools and photocatalytic cascades. A sequence-level handle on cofactor selection means that protein engineers can now rationally swap cofactor identity in designed enzymes, effectively reprogramming the electrochemical capabilities of a catalytic scaffold without altering its overall fold. This could accelerate the design of biocatalysts for green chemistry, where replacing metal catalysts and harsh reagents with enzyme-based alternatives is a major industrial goal.

From an evolutionary standpoint, the findings raise fascinating questions about how and why biology expanded its redox cofactor repertoire in the first place. The canonical cofactors are ancient, likely predating the last universal common ancestor, and their chemistry is deeply woven into core metabolism. Noncanonical cofactors, by contrast, appear to have arisen as evolutionary innovations in specific ecological and metabolic contexts—perhaps to exploit new redox niches, to escape the thermodynamic constraints of shared metabolic pools, or to protect specialized pathways from cross-talk with housekeeping chemistry. The presence of a dedicated sequence motif suggests that cofactor innovation was accompanied by co-evolution of the protein binding environment, producing a heritable, recognizable signature that could be propagated across enzyme families through duplication and divergence. In this sense, the motif is a fossil record of chemical innovation, preserving in amino acid sequence the memory of evolutionary experiments in electron transfer.

The study also serves as a cautionary tale for genome annotation. Most automated pipelines assign enzyme function by homology, and a protein that resembles a flavin-dependent monooxygenase is typically annotated as such, regardless of which cofactor it actually employs. If a substantial fraction of these enzymes in fact use noncanonical cofactors, then large swaths of existing functional annotations may be subtly or substantially wrong, with consequences for metabolic modeling, pathway reconstruction and the interpretation of gene-expression data. The motif provides a corrective lens, allowing annotators to flag proteins whose cofactor assignments deserve experimental scrutiny. As the authors and commentators in the field note, the lesson is broader: the most abundant cofactors are not necessarily the only ones, and assumptions baked into databases can obscure entire layers of biochemical diversity.

Looking forward, the identification of this sequence motif is likely to catalyze a wave of discovery across several fronts. Experimentalists will purify and characterize motif-bearing enzymes from diverse organisms, likely uncovering new cofactor structures and new reaction types. Computational biologists will refine the motif definition, searching for related patterns that govern the use of other exotic cofactors, and integrating these signals into machine-learning models of enzyme function. Structural biologists will determine how the motif residues reshape the cofactor-binding pocket at atomic resolution, providing design principles for engineered catalysts. And natural products chemists will revisit orphan biosynthetic gene clusters with fresh eyes, suspecting that many of the unexplained transformations encoded within them depend on redox chemistry that no one thought to look for. What began as a search for a short string of amino acids has ended with a map pointing toward a vast, unexplored territory of enzyme chemistry—one that has been hiding in plain sight within the genomes of organisms all around us, waiting only for the right pattern to reveal it.

Subject of Research: A conserved sequence motif that enables natural enzymes to use noncanonical redox cofactors

Article Title: A sequence motif enables widespread use of noncanonical redox cofactors in natural enzymes

Article References: Saleh, S., Hsu, N.-H., Luu, E., Martin, V. C., Ng, H. J. C., Black, W. B., Zhang, S., Kim, J.-K., Sankaran, B., Tran, A. H. T., Hayes, R. L., Siegel, J. B., Qiao, F., & Li, H. (2026). A sequence motif enables widespread use of noncanonical redox cofactors in natural enzymes. Nature Chemical Biology. https://doi.org/10.1038/s41589-026-02315-w

Image Credits: AI Generated

DOI: 10.1038/s41589-026-02315-w

Keywords: redox cofactors, sequence motif, enzymes, flavin, natural product biosynthesis, genome annotation, enzyme engineering, deazaflavin F420, biocatalysis, protein evolution, biosynthetic gene clusters, Nature Chemical Biology