CRISPR-Cas9, an RNA-guided immune system, functions specifically in bacteria while controlling autoimmunity. However, its application to genome editing often causes deleterious off-target cleavages. Here, by sequencing C...CRISPR-Cas9, an RNA-guided immune system, functions specifically in bacteria while controlling autoimmunity. However, its application to genome editing often causes deleterious off-target cleavages. Here, by sequencing CRISPR RNAs (crRNAs), we discovered abasic modifications that naturally suppress off-target self-cleavages from activated Cas9 in Streptococcus pyogenes (SpCas9). Bacteriophage infection induces oxidative stress, preferentially oxidizing the 5' end of crRNAs into abasic modifications. Mechanistically, abasic substitutions at the 5' end reduce off-target effects by limiting base pairing while preserving SpCas9-interacting backbones to maintain on-target efficiency. Abasic extensions at the 5' end reduce off-target effects by sterically constraining SpCas9 but retain on-target activity by avoiding extra base pairs. Moreover, these approaches can be combined (abasic substitution and extension), enhancing SpCas9 fidelity by increasing mismatch intolerance at the protospacer-adjacent motif-distal region and outperforming SpCas9 variants. Biologically inspired, we developed abasic chemical modifications for guide RNAs that improve CRISPR-Cas9 genome-editing specificity, demonstrating potential for in vivo application.
Livnah E, Suss O, Rogel A
… +19 more, Gilat A, Abdan Y, Villegas JA, Gabizon R, Nadir A, Shamir Y, Steinman NY, Tivon B, Albeck S, Unger T, Golani O, Goliand I, Elad N, Carvalho S, Shurrush K, Barr H, Margulies D, Levy ED, London N
Molecules that facilitate protein-protein interactions are immensely impactful. However, such compounds typically rely on accessory proteins to function, such as E3 ligases for targeted degradation, which may restrict th...Molecules that facilitate protein-protein interactions are immensely impactful. However, such compounds typically rely on accessory proteins to function, such as E3 ligases for targeted degradation, which may restrict their scope or lead to resistance. We alleviate the need for accessory proteins with a strategy that exploits protein symmetry as a selective vulnerability and is widely applicable because of the ubiquitous nature of homomeric proteins. We target homomeric proteins with PINCHs (polymerization-inducing chimeras)-bifunctional molecules composed of two linked ligands that bridge homomers and trigger their supramolecular assembly into insoluble polymers. We design PINCHs that achieve efficient polymerization of four targets. In cells, we observed that a PINCH targeting Keap1 exhibited a longer duration of action and a PINCH targeting BCL6 displayed selective lowering of B cell viability compared to their monomeric parents. Our results highlight PINCHs as a novel and general strategy to modulate and knock out protein function.
Pseudaminic acids (Pse) are a family of carbohydrates found within bacterial lipopolysaccharides, capsular polysaccharides and glycoproteins that are critical for the virulence of human pathogens. However, a dearth of ef...Pseudaminic acids (Pse) are a family of carbohydrates found within bacterial lipopolysaccharides, capsular polysaccharides and glycoproteins that are critical for the virulence of human pathogens. However, a dearth of effective tools for detecting and enriching Pse has restricted study to only the most abundant Pse-containing glycoconjugates. Here we devise a synthesis of α- and β-O-pseudaminylated glycopeptides to generate 'pan-specific' monoclonal antibodies (mAbs) that recognize α- and β-configured Pse with diverse N7 acyl groups, as well as its C8 epimer (8ePse), presented within glycans or directly linked to polypeptide backbones. Structural characterization reveals the molecular basis of Pse recognition across a range of diverse chemical contexts. Using these mAbs, we establish a glycoproteomic workflow to map the Pse glycome of Helicobacter pylori, Campylobacter jejuni and Acinetobacter baumannii strains. Finally, we demonstrate that the mAbs recognize diverse capsule types in multidrug-resistant Acinetobacter baumannii and enhance phagocytosis to eliminate infections in mice.
The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widely found across the proteome and regulates diverse cellular processes, from transcription and translatio...The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widely found across the proteome and regulates diverse cellular processes, from transcription and translation to signal transduction and metabolism. However, most functional studies to date have focused on individual modifications, overlooking other simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here we describe networking of O-GlcNAc transferase interactors and substrates (NOTISE), a systems-level approach that monitors O-GlcNAcylation rapidly and comprehensively across the proteome to reveal important functional and regulatory relationships. The NOTISE method integrates affinity purification-mass spectrometry and site-specific chemoproteomic technologies with network generation to connect putative upstream regulators and downstream targets of O-GlcNAcylation. The resulting data-rich networks identify critical conserved activities of O-GlcNAcylation and tissue-specific functions. This holistic and unbiased approach provides a broadly applicable framework to catalyze investigations into the functional roles of coordinated, multisubstrate PTMs in specific cellular and physiological contexts.
Zhao J, Luebbers A, Savransky S
… +11 more, Lin TY, Cheng N, Wilcox A, Janicot R, Green E, Sharma A, Maziarz M, Varelas X, Irannejad R, Vilardaga JP, Garcia-Marcos M
Gα serves as the prototypical signal transducer for G-protein-coupled receptors (GPCRs) and is the heterotrimeric G protein most frequently mutated in cancer. The classical view of the plasma membrane as the only cellula...Gα serves as the prototypical signal transducer for G-protein-coupled receptors (GPCRs) and is the heterotrimeric G protein most frequently mutated in cancer. The classical view of the plasma membrane as the only cellular location where GPCR signal transduction occurs has been challenged by evidence suggesting that G also signals from intracellular compartments. However, progress on this topic has stalled because of insufficient approaches with adequate spatiotemporal resolution. Here we describe genetically encoded probes and cell-penetrating compounds that block the effector-binding site of active Gα in cells to prevent signal propagation at discrete subcellular locations, at user-specified times and across diverse experimental conditions. Using these tools, we show direct evidence of Gα-mediated signaling on intracellular organelles, unique spatiotemporal features of signaling by Gα oncomutants and specific regulation of physiologically relevant responses in cardiac or immune cells. These findings pave the way to harnessing the spatiotemporal modulation of G signaling and its untapped therapeutic potential.
Chen GY, Deng C, Chenoweth DM
… +1 more, Lampson MA
Nat Chem Biol
· 2026 Jan · PMID 41617855
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Anaphase chromosome segregation depends on forces exerted by spindle microtubules. Current models propose two force-generating mechanisms: kinetochore-microtubule (kMT) depolymerization pulls chromosomes toward spindle p...Anaphase chromosome segregation depends on forces exerted by spindle microtubules. Current models propose two force-generating mechanisms: kinetochore-microtubule (kMT) depolymerization pulls chromosomes toward spindle poles (anaphase A), while antiparallel microtubule sliding in the central spindle further separates sister chromosomes by elongating the spindle (anaphase B). Experimental evidence in cells supports the sliding mechanism but contributions of the depolymerization mechanism remain unclear. We show that kMT depolymerization limits spindle elongation rather than moving chromosomes apart. We developed a chemical optogenetic approach to recruit microtubule depolymerases to kinetochores at anaphase onset, thereby increasing kMT depolymerization rates without perturbing earlier stages of mitosis. We find that increased depolymerization slows the velocity at which spindle poles move apart without changing kinetochore separation velocities. Our findings support a model in which kinetochores selectively couple to central spindle microtubules parallel to their kMTs, such that antiparallel sliding drives chromosome segregation while kMT depolymerization pulls poles inward.
Siahaan V, Weissova R, Karhanova A
… +10 more, Lanska E, Ruiz-Estrada MJ, Pukajová B, Dostál V, Henriot V, Janke C, Libusová L, Braun M, Balastik M, Lansky Z
Nat Chem Biol
· 2026 May · PMID 41593416
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Tau is an axonal microtubule-associated protein. Tau interaction with microtubules is regulated by phosphorylation. Hyperphosphorylation of tau is implicated in microtubule destabilization related to neurodegenerative di...Tau is an axonal microtubule-associated protein. Tau interaction with microtubules is regulated by phosphorylation. Hyperphosphorylation of tau is implicated in microtubule destabilization related to neurodegenerative disorders. However, how tau phosphorylation leads to microtubule destabilization is unknown. Recently, it was shown that tau molecules on microtubules cooperatively assemble into cohesive layers termed envelopes. Tau envelopes protect microtubules against degradation by microtubule-severing enzymes, suggesting a functional link between envelopes and microtubule stability. Here we show that tau phosphorylation has deleterious effects on the microtubule-protective function of tau envelopes. Using reconstitution and live-cell experiments, we found that tau phosphorylation destabilizes tau envelopes and decreases their integrity, leading to reduced microtubule protection against microtubule-severing enzymes. Our data suggest that a perturbation of microtubule homeostasis linked to tau hyperphosphorylation in neurodegeneration can be explained by the disassembly and impaired functionality of the tau envelopes.
Zhang Q, Sun T, Yu F
… +31 more, Liu W, Gao J, Chen J, Zheng H, Liu J, Miao C, Guo H, Tian W, Su M, Guo Y, Liu X, Pei Y, Wang Z, Chen S, Mu C, Lam SM, Shui G, Li Z, Yu Z, Zhang Y, Chen G, Lu C, Midgley AC, Li C, Bian X, Liao X, Wang Y, Xiong W, Zhu H, Li Y, Chen Q
CRISPR-Cas systems are transformative tools for gene editing that can be tuned or controlled by anti-CRISPRs (Acrs)-phage-derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that can inhibit biotechnologi...CRISPR-Cas systems are transformative tools for gene editing that can be tuned or controlled by anti-CRISPRs (Acrs)-phage-derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that can inhibit biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we describe a highly successful and rapid approach that leverages de novo protein design to develop new-to-nature proteins for controlling CRISPR-Cas activity. Here, using Leptotrichia buccalis CRISPR-Cas13a as a representative example, we demonstrate that Acrs designed using artificial intelligence (AIcrs) are capable of highly potent and specific inhibition of CRISPR-Cas13a nuclease activity. We present a comprehensive workflow for design validation and demonstrate AIcr functionality in controlling CRISPR-Cas13 activity in bacterial and human cells. The ability to design bespoke inhibitors of Cas effectors will contribute to the ongoing development of CRISPR-Cas tools in diverse applications across research, medicine, agriculture and microbiology.
Zhou JX, Shao ZY, Zhang L
… +19 more, Guo JN, Wang M, Xu Q, Wang YQ, Xu Q, Zhou D, Ren SX, Yu YH, Lu ZH, Pang GZ, Cao Y, Liu YL, Zhou B, Ji HB, Chen YH, Wu HP, Xu GL, Zhang L, Du YR
Thymine DNA glycosylase (TDG) is a multifaceted protein involved in base-excision repair, DNA demethylation and transcriptional regulation, with key roles in embryonic development and tumorigenesis. However, the mechanis...Thymine DNA glycosylase (TDG) is a multifaceted protein involved in base-excision repair, DNA demethylation and transcriptional regulation, with key roles in embryonic development and tumorigenesis. However, the mechanisms underlying its role in cancer progression and the therapeutic applications targeting TDG remain largely unknown. Here we demonstrate that targeting TDG induces synthetic lethality in p53-deficient cancers. We developed C-271, a first-in-class, small-molecule inhibitor that covalently binds to TDG, disrupting its DNA-binding capability. C-271 exhibits potent therapeutic efficacy in suppressing p53-deficient tumors. Mechanistically, TDG and p53 redundantly promote the transcription of DHX9, an RNA helicase that resolves double-stranded RNA (dsRNA). TDG inhibition in p53-deficient cancer cells leads to DHX9 downregulation and, thus, aberrant dsRNA accumulation, which activates the RIG-I/MDA5-MAVS sensing pathway, resulting in tumor suppression and enhanced antitumor immunity. These findings highlight the synthetic lethality between TDG and p53, positioning TDG inhibition as a promising therapeutic strategy for p53-deficient cancers.
Geohring IC, Chai P, Iyer BR
… +8 more, Ton WD, Yang J, Ide AH, George SC, Bagri JS, Baird SV, Zhang K, Markus SM
Nat Chem Biol
· 2026 Apr · PMID 41571912
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Dynein-1 is a microtubule motor that transports numerous cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state before its assembly with dynactin and a cargo adaptor. Studies sugges...Dynein-1 is a microtubule motor that transports numerous cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state before its assembly with dynactin and a cargo adaptor. Studies suggest that Lis1 may relieve dynein's autoinhibited state, although evidence for this is lacking. We first determined the rules governing dynein-Lis1 binding, revealing that their binding affinity is regulated by the nucleotide-bound states of each of three nucleotide-binding pockets within dynein. We also found that distinct nucleotide 'codes' coordinate their binding stoichiometry by impacting binding affinity at two different sites within the dynein motor domain. Electron microscopy revealed that a 1 dynein:1 Lis1 complex directly promotes an uninhibited conformational state of dynein, whereas a 1:2 complex resembles the autoinhibited state. Cryo-electron microscopy revealed that the structural basis for Lis1 opening dynein relies on interactions with the linker domain. Our work reveals the biochemical basis by which Lis1 relieves dynein autoinhibition.
Li Z, Chawla H, Di Vagno L
… +22 more, Ní Cheallaigh A, Critcher M, Sammon D, Gonzalez-Rodriguez E, Briggs DC, Chung N, Chang V, Mahoney KE, Cioce A, Bineva-Todd G, Wang PY, Liu YC, Murphy LD, Chen YH, Narimatsu Y, Miller RL, Willems LI, Malaker SA, Huang ML, Miller GJ, Hohenester E, Schumann B
Nat Chem Biol
· 2026 Apr · PMID 41559400
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Mammalian cells receive signaling instructions through interactions on their surfaces. Proteoglycans are critical to these interactions, carrying long glycosaminoglycans that recruit signaling molecules. Biosynthetic red...Mammalian cells receive signaling instructions through interactions on their surfaces. Proteoglycans are critical to these interactions, carrying long glycosaminoglycans that recruit signaling molecules. Biosynthetic redundancy in the first glycosylation step by two xylosyltransferases XT1/2 complicates annotation of proteoglycans. Here we develop a chemical genetic strategy that manipulates the glycan attachment site of cellular proteoglycans. Through a bump-and-hole tactic, we engineer the two isoenzymes XT1 and XT2 to specifically transfer the chemically tagged xylose analog 6AzGlc to target proteins. The tag contains a bioorthogonal functionality, allowing to visualize and profile target proteins in mammalian cells. Unlike xylose analogs, 6AzGlc is amenable to cellular nucleotide-sugar biosynthesis, establishing the XT1/2 bump-and-hole tactic in cells. The approach allows pinpointing glycosylation sites by mass spectrometry and exploiting the chemical handle to manufacture proteoglycans with defined glycosaminoglycan chains for cellular applications. Engineered XT enzymes permit an orthogonal view into proteoglycan biology through conventional techniques in biochemistry.
Modifications at the wobble position of transfer RNA (tRNA) are critical for accurate codon recognition and efficient translation. 5-Hydroxyuridine serves as a key intermediate for more complex wobble uridine derivatives...Modifications at the wobble position of transfer RNA (tRNA) are critical for accurate codon recognition and efficient translation. 5-Hydroxyuridine serves as a key intermediate for more complex wobble uridine derivatives commonly found in bacterial tRNAs and is synthesized by either prephenate-dependent TrhP or dioxygen-dependent TrhO. Despite its biological importance, structural and mechanistic insights into these enzymes have remained elusive. Here, we report the cryo-electron microscopy structure of Bacillus subtilis TrhO-tRNA complex. Combined with biochemical analyses, our results reveal that TrhO functions without any metal or organic cofactor, unlike most other oxygenases. We propose that the conserved C179 reacts with dioxygen to form a thiohydroperoxy intermediate, which is cleaved to produce 5-hydroxyuridine and a sulfenic acid at C179. The oxidized cysteine subsequently forms a disulfide bond with the adjacent C185, protecting the catalytic cysteine from irreversible overoxidation. These findings broaden our understanding of cofactor-independent dioxygen use in aromatic ring hydroxylation.
Müller M, Niemeyer K, Ojha NK
… +17 more, Porav SA, Vinayagam D, Urban N, Büchau F, Oleinikov K, Makke M, Bauer CC, Johnson AV, Muench SP, Zufall F, Bruns D, Schwarz Y, Raunser S, Leinders-Zufall T, Bon RS, Schaefer M, Thorn-Seshold O
Nat Chem Biol
· 2026 Feb · PMID 41545580
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Precisely probing the endogenous roles of target proteins is crucial for biological research. Photochemical tools can be photoactuated with high spatiotemporal resolution but often they are unreliable in vivo because spa...Precisely probing the endogenous roles of target proteins is crucial for biological research. Photochemical tools can be photoactuated with high spatiotemporal resolution but often they are unreliable in vivo because spatiotemporal variations of reagent concentration result in inhomogeneous bioactivity. We now describe ideal efficacy photoswitching, a paradigm that internally compensates for reagent concentration by self-competitive binding, allowing purely wavelength-dependent chromocontrol over bioactivity that is consistent from cell culture to deep tissues. We demonstrate this with photoswitches for endogenous transient receptor potential (TRP) C4 and C5 ion channels, reproducibly delivering strong agonism under 360-nm illumination, weak agonism under 385-nm illumination and strong antagonism under 440-nm illumination. These ligands unlock a range of high-precision investigations in TRP biology, from neuronal activity to exocytosis, reproductive signaling and smooth muscle contractility. The ideal efficacy photoswitching paradigm should also unlock high-performance chromocontrol over a wide range of sensory or signaling channels and receptors even in vivo.