Nature biotechnology最新文献

The degradation of cell membrane and extracellular proteins with lysosome-targeting chimeras (LYTACs) is limited by nonrecyclable, receptor-dependent mechanisms that shuttle proteins to lysosomes, restricting the broad use of this emerging technology. Here we developed a recyclable chimera composed of a polyzwitterion and protein of interest (POI) ligand for protein degradation. This chimera could interact with the cell membrane to trigger macropinocytosis together with the POI in a receptor-independent manner. Furthermore, it can dissociate from the POI in the acidic endocytic compartments and subsequently be exocytosed through the endoplasmic reticulum-Golgi transcytosis pathway. Ultimately, the exocytotic chimera initiates the next round of targeted protein degradation. These macropinocytosis-mediated recyclable LYTACs (McR-TACs) durably degrade the cell membrane protein (programmed cell death ligand 1) or the extracellular protein (macrophage migration inhibitory factor) in a triple-negative breast cancer mouse model, thereby inhibiting the tumor growth. Collectively, McR-TACs show the potential of leveraging natural transport pathways to create recyclable protein degraders with wide-ranging applications.

Silicate mineral weathering (dissolution) is a scalable strategy for capture and storage of CO₂ but is too slow for industrial deployment. Bacteria can accelerate mineral dissolution by secreting siderophores, molecules that solubilize iron released from the mineral. Here we investigate how to deploy siderophore-producing bacteria at scale to continuously enhance dissolution of the mineral olivine. We demonstrate that natural genetic regulation precludes continuous siderophore production in mineral bioreactors. To overcome this limitation, we engineer the marine bacterium Alteromonas macleodii for enhanced siderophore production, conferring a 2.6-fold increase in the rate of olivine dissolution. Life-cycle analysis indicated that renewable feedstocks and minimal replenishment of modified cells are critical to achieve net CO₂ removal at scale. With these guidelines, we constructed pilot-scale continuous mineral bioreactors that use unprocessed seawater and a renewable acetate feedstock to weather 4 kg of olivine. In reactors with engineered cells, we directly measured removal of 0.50 g CO₂ per day from the air through alkalinity generation.

UniFrac measures phylogeny-aware differences between microbiome samples but scales poorly with modern dataset sizes. We introduce an algorithm, DartUniFrac, and a near-optimal implementation with graphics processing unit acceleration that is up to three orders of magnitude faster than UniFrac and scales to millions of samples (pairwise) and billions of taxa. DartUniFrac connects UniFrac with weighted Jaccard similarity and exploits sketching algorithms for fast computation.

Replacing large-scale fragments in human cells remains a substantial challenge. Here, we present a programmable gene replacement tool, named prime assembly (PA), which adapts prime editors to produce one or two pairs of 3'-flaps on both the genome and donor DNA. These 3'-flaps anneal to each other precisely, similar to Gibson assembly in DNA oligonucleotides, allowing megabase-scale genomic excision and/or kilobase-scale donor insertion at the gene of interest. PA accepts DNA plasmids and linear double-stranded DNA as donors, ranging from 1.0 to 6.5 kb in size. We demonstrate an efficiency of up to 57.8% in replacing endogenous sequences with a 2.9-kb donor DNA fragment in HEK293T cells, with an accuracy of >90% for integrated PA fragments. Furthermore, PA enables site-specific chimeric antigen receptor integration with up to 28.1% efficiency in primary human T cells. When PA containing a GFP donor is delivered to mice by hydrodynamic injection, an average integration efficiency of 4.3% is measured in GFP-positive hepatocytes.

Methods for precise genomic DNA insertion that avoid double-strand breaks (DSBs) are constrained by limited throughput or the need for multistep editing. Here we report donor-complementary prime editing (DoPE), which combines a 3'-overhang double-stranded DNA (odsDNA) donor with a pair of overhang-complementary prime editing guide RNAs (opegRNAs) and a PE2* prime editor to achieve precise insertion of DNA sequences up to 12.5 kilobases (kb). Using one opegRNA pair and donor pools constructed from synthesized single-stranded oligonucleotides, we demonstrate in situ saturation mutagenesis across a targeted EGFP region at both amino acid and nucleotide resolutions. DoPE employing short (approximately 30-nucleotide) overhangs supports various insertions ranging from small fragments to those exceeding 10 kb. Furthermore, we replace mutant exons of PRKCSH, either individually or simultaneously, to correct diverse mutations, establishing a mutation-agnostic approach that corrects distinct alleles uniformly in vitro. Our study demonstrates DoPE as a one-step, DSB-free and library-compatible method for precise insertion of large DNA fragments without requiring recombinases or transposases.

Gut Clostridia species, including commensal members of the Clostridiaceae and Lachnospiraceae families, maintain microbiota homeostasis and influence human health and disease; however, adequate genetic toolsets to study abundant but nonmodel gut Clostridia are lacking. Here we present a set of transferable and modular genetic toolsets that function broadly across phylogenetically diverse gut Clostridia. We first identify a panel of strong constitutive promoters that drive robust gene expression across diverse clostridial strains. We then develop an inducible promoter system that enables precise, tunable gene regulation and facilitates the implementation of CRISPR-Cas gene-deletion systems. We apply this system for targeted and reversible control of trimethylamine and deoxycholic acid production, two microbiota-derived metabolites implicated in host lipid metabolism and diseases, in mice. This robust genetic toolkit for nonmodel gut Clostridia enables functional studies to causally link microbiota genes to host physiology and disease, paving the way for therapeutic genetic engineering of microbiota.

Efficient protein engineering is constrained by vast sequence space and limited experimental throughput, particularly for protein families that lack large mutational datasets. Here we combine Fanzor2 (Fz2) ortholog discovery, ωRNA scaffold engineering and EvoMax, a model-guided prioritization strategy for sparse-data engineering of compact eukaryotic Fz2 nucleases. EvoMax integrates iterative experimental profiling with Gaussian process regression, protein language models and inverse folding to navigate complex sequence-to-fitness landscapes. Applied to eukaryotic Fz2 nucleases, this strategy yielded a high-performance variant, FanzMAX v3-hLa, achieving up to 97% editing efficiency at the best-performing endogenous locus and a mean editing efficiency of ~33% across 19 endogenous loci, outperforming the established compact genome editors enNlovFz2 and enCnCas12f1 by more than 2.6-fold. In vivo editing of hPCSK9 in humanized mice supported the translational potential of optimized Fz2 editors. Together, these results establish EvoMax as an integrated strategy for engineering compact eukaryotic Fz2 genome editors and identify FanzMAX v3-hLa as a high-efficiency programmable nuclease for mammalian genome editing.