The Gene Ontology (GO) knowledgebase https://geneontology.org is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Colouration of textiles is responsible for 3% of global greenhouse gas emissions and 20% of global wastewater generation. An estimated 20% of the dyes and pigments used in textile colouration is lost to wastewater. Synthetic dyes and pigments, along with many of the chemicals added to their formulations, are

nonbiodegradable, persistent, and bioaccumulative in aquatic

ecosystems, posing signi cant risks throughout the food chain. Regulatory bodies in both Europe and the United States are continuing to ban, restrict, and phase out many synthetic dyes and pigments. The EU recently banned a significant number of common textile dyes known to release carcinogenic compounds,

while in the United States, 8 common synthetic food dyes are

being targeted for immediate ban in the US food supply, with the FDA planning to phase out all remaining synthetic food dyes. While bio-based alternatives are available on the market, they are

currently more expensive, restricting their application to niche product applications that can absorb the price premium. The total market size for dyes and pigments is more than US$ 50 billion and is growing at a rate of 3–10% annually. The ‘cost of being unsustainable’ is increasing rapidly, particularly in the EU, as new regulations make the use of hazardous chemicals more difficult

and expensive. This is driving a shift toward the use of more sustainable chemicals.

Base editors enable precise genome modification but are constrained by bystander edits that limit their applicability. Existing strategies to enhance precision often compromise efficiency and remain highly sequence dependent. Here we present a parallel engineering approach that optimizes both guide RNAs and the deaminase enzyme to minimize bystander editing without sacrificing activity. We designed a library of 3′-extended guide RNAs and identified context-dependent variants that improved specificity. Using a precision-driven phage-assisted evolution system and protein language models, we evolved adenine base editor variants two- to threefold more precise than adenine base editor ABE8e while maintaining high efficiency across a library of thousands of human pathogenic contexts in vitro. Our findings establish a scalable framework for precision engineering of base editors, addressing a major challenge in genome editing. Base editors are made more precise through deaminase and gRNA engineering.

Anaerobic ammonium oxidizing bacteria in the class “Candidatus Brocadiia” in the Planctomycetota are the only known group of bacteria capable of producing energy by coupling the oxidation of ammonium to the reduction of nitrite within a unique bacterial organelle called the anammoxosome. Due to the lack of homologs in other species, it is hypothesized that the key enzyme in this process, the hydrazine synthase complex, originated by de novo birth. We performed extensive searches for proteins that exhibited similarity in sequence and structure to the hydrazine synthase subunits and identified distantly related homologs in anaerobic bacteria from the phyla Planctomycetota and Desulfobacterota. However, key residues of importance for the enzymatic function were not conserved, rejecting the hypothesis that the identified genes represent previously unrecognized anammox bacteria. Phylogenetic analyses indicate that the anammox pathway has been assembled from genes acquired by horizontal gene transfer from a variety of anaerobic bacteria. The ancestral states of enzymes in the hydroxylamine oxidoreductase family were inferred, and transitions between reductive and oxidative forms of the enzymes were mapped onto the phylogenetic tree. Finally, it is shown that the signal sequences of key enzymes in the anammox pathway are able to transport a reporter gene into the periplasm of Escherichia coli cells. In conclusion, our findings suggest that the hydrazine synthase complex has evolved from already existing heme-binding periplasmic proteins and that the anammoxosome has an endogenous origin.

Prime editing (PE) enables the precise installation of intended base substitutions, small deletions or small insertions into the genome of living cells. While the use of Cas9 nickase can avoid DNA double-strand breaks (DSB), undesired insertions and deletions (indels) often accompany the correct edits, particularly when PE activity increased. Here we show that the anti-CRISPR (Acr) protein AcrIIA5 can significantly enhance PE activity by up to 8.2-fold while markedly reducing byproduct indels. Further investigation reveals that AcrIIA5 can promote PE across various approaches (PE2, PE3, PE4, PE5, and PE6), edit types (substitutions, insertions and deletions), and endogenous loci. Mechanistically, AcrIIA5 appears to inhibit the re-nicking activity of PE complex rather than enhancing the core editing machinery itself, suggesting a distinct mode of interaction with Cas9. Overall, we demonstrate that a known “inhibitor” Acr protein can unexpectedly acting as an “enhancer” of CRISPR/Cas-based genome editing, providing an effective strategy to optimize PE specificity and activity. Prime editing enables precise genetic modification but often suffers from unwanted byproducts. Here, authors show that the anti-CRISPR protein AcrIIA5 unexpectedly enhances prime editing efficiency while reducing unintended indels, offering an effective strategy to improve activity and specificity.

Directed evolution facilitates functional adaptations through stepwise changes in sequence that alter protein structure. While most campaigns yield solutions that maintain the framework of a rigid protein architecture, a few have produced enzymes with more notable structural differences. One example is a polymerase that was evolved to synthesize threose nucleic acid (TNA) with near-natural activity. Understanding how this enzyme arose provides a model for studying pathways that guide enzymes toward more productive regions of the fitness landscape. Here, we trace the evolutionary trajectory of an unnatural polymerase by solving crystal structures of key intermediates along the pathway and evaluating their biochemical activity. Contrary to the view that fidelity is a product of increased catalytic efficiency, we find that accuracy and catalysis are decoupled activities guided by separate ground-state and transition-state discrimination events. Together, these results offer a glimpse into the forces responsible for shaping the emergence of new enzyme functions. Engineering polymerases to synthesize alternative genetic polymers remains a challenging problem in synthetic biology. The current study offers insights into the structural and biochemical changes responsible for improving the fidelity and catalytic activity of a laboratory evolved TNA polymerase.

Extracting fungal hyphae with their naturally associated microbiota from soil samples presents a significant challenge due to their small size, typically in the micrometer range, and the formation of dynamic fungal networks. We combined elements of previous protocols and automated the wet-sieving steps of the methodology to efficiently extract fungal hyphae from various soil types, including natural loamy soils. This approach reduces manual handling, minimizes operator-dependent variability, and shortens processing time by up to 2.5-fold. Unlike earlier methods that require sand or glass bead supplementation, which can introduce artificial conditions and limit large-scale field applications, our Sieving and Sucrose Centrifugation (SSC) method avoids these drawbacks. The SSC technique enables both quantification of hyphal length density (HLD) and, importantly, preserves surface-associated microbes for downstream analyses. Among the tested methods, SSC yielded the highest hyphal length density. Using a combination of microscopy, molecular techniques, and next-generation sequencing (NGS), we demonstrate that this method allows targeted study of bacteria tightly attached to fungal hyphae. Furthermore, the SSC approach effectively enriched fungal hyphae from a highly diverse soil community, establishing a dependable tool for advancing research on fungal hyphae as microbial hotspots in soil ecosystems.

Antibiotic resistance stands as a formidable global challenge to public health. Herein, we present a bacterial nanoinducer (bacNID) designed for targeted protein degradation in treating bacterial infections. Specifically, bacNID is engineered by grafting targeting peptides of MurD and SspB onto gold nanoparticles (GNPs). MurD plays a pivotal role in peptidoglycan production for cell wall synthesis, while SspB recruits SsrA-tagged proteins for degradation by ClpXP protease. The effectiveness of bacNIDs in targeted MurD degradation via ClpXP is demonstrated across both Gram-positive and Gram-negative bacterial strains. Importantly, prolonged exposure to bacNIDs does not result in the acquisition of resistance in either Staphylococcus aureus (S. aureus) or Salmonella typhimurium (S. typhimurium), even after 25 successive treatment passages. This stands in stark contrast to the rapid emergence of robust resistance observed with norfloxacin, evidenced by a 243-fold reduction in antibacterial activity against S. aureus after just 15 passages, and a 7410-fold decrease in activity against S. typhimurium over 22 passages. Moreover, the antimicrobial potential of bacNIDs is evaluated in vivo using S. aureus-infected nonhealing skin and corneal wounds. In summary, this study unveils a potent nanotechnology-driven strategy for targeted bacterial protein degradation with promising implications for in vivo antimicrobial applications. In this work, authors present a nanoinducer (bacNID), which enables targeted bacterial protein degradation via ClpXP, leading to the effective treatment of bacterial infection (Staphylococcus aureus and Salmonella typhimurium) without inducing resistance.