Research Briefing in 2025

Radical Fe^II/α-ketoglutarate-dependent halogenases are promising biocatalysts for C(sp³)–H functionalization, which can replace a substrate H atom with a bound anion. In this study, we have shown that the amino acid halogenase HalA uses dynamic active site coordination to control the reaction cycle, promoting both C–H activation and subsequent anion transfer.

Clostridium autoethanogenum produces ethanol from waste gases, but the biosynthetic pathway has been debated. Now, a combination of structural and biochemical data confirms that a key step in the ethanol biosynthesis pathway is acetate reduction by a tungsten-dependent aldehyde:ferredoxin oxido-reductase. This thermodynamically unfavorable reaction is counterbalanced by the coupling of ethanol synthesis with CO oxidation.

We developed the prime editing tool PIE, which produces precise inversions of large genomic segments and chromosomal structural variations in mammalian cells. PIEv3b achieves high inversion efficiency and outperforms nuclease- and integrase-based methods, enabling chromosome reconfiguration from metacentric to telocentric forms.

The discovery of macrocyclic peptide therapeutics has been slow. We introduce RFpeptides, a deep learning method that enables the de novo design of macrocyclic peptide binders to therapeutic targets. The designed macrocycles bind their respective protein targets with high affinity and atomic-level accuracy.

We present a versatile, chemo-ribosomal approach to generating isolable quantities of protein-derived biopolymers containing site-specific backbone modifications, including β-, γ- and δ-peptide linkages. Two of these extended backbones would be difficult to establish by alternative strategies in folded, full-length proteins generated in cells.

We developed a programmable RNA acetylation system by fusing dCas13 with an engineered NAT10 variant, enabling robust and specific installation of N⁴-acetylcytidine (ac⁴C) on target RNAs in cultured cells and live animals. This system facilitated functional studies of RNA acetylation and revealed ac⁴C has a distinct role in regulating transcript subcellular localization.

We uncovered the function of a cell-bound biosurfactant, a glycine-glucolipid from Alcanivorax borkumensis that is synthesized via an unusual non-ribosomal peptide synthetase pathway. The glycine-glucolipid enhances microbial adhesion to oil droplets, enabling rapid degradation of the oil. Our research provides insights into advanced bioremediation strategies.

Negamcyin, a decades-old antibiotic, is a promising lead compound for the development of drugs for treatment of Gram-negative pathogens and hereditary diseases. We identified its biosynthetic gene cluster and found a new heme-dependent enzyme that directly forms its nitrogen–nitrogen bond from glycine and nitrite.

We developed a ligand-responsive solid-state condensate platform for on-demand spatiotemporal control of gene expression in mammalian cells. In particular, the modular design of the condensates enabled spatiotemporal capture and manipulation of DNA, RNA and protein in engineered nuclear condensate structures as an efficient alternative for regulating gene expression.

Poly(ester amide)s (PEAs) have various applications but their synthesis is currently limited to chemical methods. Now, the biosynthesis of various PEAs in engineered Escherichia coli is presented. The PEAs incorporate different amino acid monomers in varying fractions, which influences their physical, thermal and mechanical properties.

The small molecule Ebio3 inactivates the ‘non-inactivating’ potassium channel KCNQ2. This inhibition occurs by a unique ‘squeeze-to-inhibit’ mechanism, rather than by blocking the channel pore as most KCNQ2 inhibitors do, offering a new mechanism for modulating voltage-gated ion channels with implications for drug discovery.

Biomolecules morph between conformations with distinct lifetimes according to their functional requirements. Mosquito-borne flaviviruses encode exoribonuclease-resistant RNAs (xrRNAs) that fold into knot-like structures to prevent exonuclease Xrn1 digestion. To achieve high Xrn1 resistance, xrRNAs contain molecular interactions with lifetimes that persist up to ten million times longer than canonical base pairs.

Measuring pharmacodynamics is crucial for drug development, but traditional pharmacodynamic studies based on tissue dissection and subsequent biochemical analysis are labor- and resource-intensive. We developed a non-invasive imaging method to efficiently and rapidly visualize the pharmacodynamics of kinase inhibitors and degraders using an engineered kinase-modulated bioluminescent indicator.

Targeting of protein aggregates is technologically challenging. We developed a phage-assisted continuous evolution platform for rapid selection of protein aggregation inhibitors from genetically encoded cyclic peptide libraries in Escherichia coli. This strategy enabled discovery of cyclic peptides that suppress the aggregation of two clinically relevant proteins, amyloid-β42 (Aβ42) and human islet amyloid polypeptide (hIAPP).

By placing artificial metalloenzymes (ArMs) in phase-separated sanctuary regions formed by their protein scaffolds in Escherichia coli, we developed various whole-cell catalysts with high power and catalytic stability. Such whole cells with sheltered ArMs achieved substantially higher turnover numbers per cell and showed catalytic activity in mice for relevant therapeutic applications.