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New methods for targeted covalent protein modification at low reactivity aspartates and glutamates are of high interest. Here, the authors report a technique inspired by the HaloTag technology, which employs a covalent conjugation reaction between ligands with a reactive chloroalkane linker and a specific aspartic acid, and use it to covalently modify lipoprotein chaperone PDEδ at a binding site glutamic acid.

Annunziato, Quan and Donckele et al. identify G3BP2 (Ras–GAP SH3 domain-binding protein 2) as a molecular glue-induced neosubstrate of the CRL4^CRBN E3 ubiquitin ligase. The CRBN–glue neosurface uses a molecular surface mimicry mechanism to recruit and degrade G3BP2 in a compound-dependent manner.

In targeted protein degradation, a degrader molecule brings a neosubstrate protein proximal to a hijacked E3 ligase for its ubiquitination. Here, pseudo-natural products derived from (−)-myrtanol—iDegs—are identified to inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs prime apo-IDO1 ubiquitination and subsequent degradation using its native proteolytic pathway.

As part of two-component systems, diguanylate cyclases (DGCs) are activated by phosphorylation. Structural and computational analyses of DgcR, a model DGC, reveal the phosphorylation-induced conformational changes and the activation mechanism likely shared by many DGCs with N-terminal coiled-coil linkers.

Base editors are made more precise through deaminase and gRNA engineering.

Bacterial multi-step phospho-relays employ receiver domains that act as intermediaries in phosphoryl shuttling. Here, the authors show that such a domain does not experience structural changes upon pseudo-phosphorylation, in contrast to the well-studied homologs in response regulators.

A small-molecule-affinity tag has been designed to mediate the selective isolation of G-quadruplex nucleic acids in a structure-dependant manner. This concept has been applied to the pull-down of G-quadruplex-containing fragments from human cells, and the methodology holds promise for the elucidation of their putative biological functions.

Lifetime-encoded materials are attractive as optical markers. Here, the authors report a design strategy for true orthogonality in encoding based on heterometallic rare-earth MOFs with independently variable lifetime and composition.

PGAM5 is a mitochondrial protein phosphatase whose functions include regulation of mitophagy and cell death. Here, the authors use x-ray crystallography and EM to show that PGAM5 forms dodecameric rings and filaments in solution, and find that PGAM5 rings are essential for catalysis and for a structural effect PGAM5 has on mitochondrial membranes, independently of catalytic activity.

The ubiquitous second messenger c-di-GMP regulates many biological processes in bacteria, including cell cycle, motility, virulence and biofilm formation. Here, Kaczmarczyk et al. develop a c-di-GMP biosensor that enables dynamic real-time tracking of c-di-GMP levels in individual living cells.

Enhanced polyamine depletion in neuroblastoma models decreases translation of mRNA codons with adenosine in the third position, reprogramming the tumour proteome away from cell cycle progression and towards differentiation.

This protocol describes the design and synthesis of CRISPR-responsive smart hydrogels and their actuation for both the controlled release of cargos (small molecules, enzymes, nanoparticles and living cells) and diagnostic applications.

A screening approach finds VH-domain antibodies that bind the SARS-CoV-2 Spike protein receptor-binding domain at its interface with host ACE2. Bi-paratopic and multivalent binders have high affinity and potency.

Plant synthetic biology offers the potential to re-engineer crops, but requires efficient methods to prepare constructs for transformation. Here Shih et al. develop jStack, a method that utilizes yeast homologous recombination and a library of DNA parts, to efficiently assemble plant transformation vectors.

GMP synthetase, a key enzyme in purine biosynthesis, is of interest for understanding purine metabolism processes and for developing therapeutic applications. Here, the authors propose a molecular mechanism and the structural basis for the catalytic activity of this enzyme.

Benjamin Raphael and colleagues report an analysis of altered subnetworks of somatic aberrations in TCGA pan-cancer data sets, including 3,281 samples from 12 cancer types, using a newly developed HotNet2 algorithm. They identify 16 significantly mutated subnetworks and provide a more comprehensive view into altered pathways, including those with known roles in cancer development.

The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.

Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here the authors show that an increase in c-di-GMP concentration modulates the activity of kinase ShkA and transcription factor TacA, thus enabling G1/S transition in Caulobacter.

Virtual screening of huge libraries is successful in identifying drug leads. Here, the authors describe a computational strategy, Chemical Space Docking, which combines docking with a reaction-based search of compounds, thereby enabling the exploration of billions of compounds and beyond.

In a randomized, placebo-controlled, stepwise dose-escalation phase 1 trial evaluating a conjugate vaccine against both typhoid and invasive non-typhoidal Salmonella infections, the vaccine was found to be safe and immunogenic in healthy adults.

A method to identify pairs of ligands that simultaneously bind to a target protein has been developed. The method uses two DNA-encoded chemical sub-libraries that self-assemble to form stable dual-display structures, and an encoding system that can be decoded by DNA sequencing and enables both ligands to be identified.

Affinity purification in Arabidopsis identified all key subunits of the outer kinetochore KMN complex. Functional analyses revealed a striking conservation of its composition and organization across kingdoms, underscoring its deep evolutionary origin.

CRISPR-Cas systems protect bacteria by capturing viral DNA as genetic memories, known as spacers. Here, authors used deep mutational scanning to identify Cas1 and Cas2 variants that enhance spacer acquisition and phage immunity, with the potential to improve CRISPR-based applications.

Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions into OFF- and ON-switches active in cells.

Some cancer cells exhibit high loads of reactive iron in lysosomes, and this feature is exploited by using fentomycin-1, a newly developed small molecule, to induce ferroptosis.

The natural product thiostrepton is known to have anticancer properties but its mechanism of action is not known. Here, it is shown that thiostrepton binds to the protein FOXM1, preventing its interaction with several gene promoters and inhibits their expression. This illustrates the druggability of transcription factors, and provides a molecular basis for targeting FOXM1.

This study examines the function of G-quadruplex DNA secondary structures in mammalian promoters, revealing that they represent core promoter elements contributing to gene regulation by nucleosome exclusion and by promoting RNA polymerase II pause–release.

Here the authors present a functional, tagged version of Rad51, which allows dynamic, in vivo studies of Rad51–ssDNA nucleoprotein filament (NPF) formation. NPFs display notable flexibility, which allows them to implement an efficient search strategy for homolog sequences amidst the crowded nucleus.

Puissant and colleagues identify a myeloid-restricted PIK3CG/p110γ–PIK3R5/p101 axis as a therapeutic vulnerability in acute myeloid leukemia and develop a proteolysis-targeting chimera to potently degrade PIK3CG and suppress AML progression.

SPTBN1 mutations cause a neurodevelopmental syndrome characterized by intellectual disability, language and motor delays, autism, seizures and other features. The variants disrupt βII-spectrin function and disturb cytoskeletal organization and dynamics.

Small-molecule ligands have been developed that covalently attach to their cognate RNA aptamers in vitro and in living cells. This strategy opens up new avenues for RNA imaging applications (for example, FRAP), for direct fluorescence detection of RNA pull-downs or for covalent RNA-targeted drug design.

Mime-seq achieves cell-type specific, methylation-based, microRNA tagging and sequencing to uncover cell-specific microRNomes in C. elegans and Drosophila.

The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes. Here the authors show that ComFC is a membrane-associated protein that participates in the transport of DNA through the cell membrane and the handling of the single-stranded DNA once delivered into the cytoplasm.

Here, the authors report de novo design, optimization and characterization of tRNAs that decode UGA stop codons in E. coli. The structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon suggests that distinct A-site ligands (tRNAs versus release factors) induce distinct conformation of the stop codon within the mRNA in the decoding center.

Two broadly reactive and inhibitory human monoclonal antibodies against the malaria parasite Plasmodium falciparum have been characterized, providing insights into immunity, prevention and treatment of severe malaria.

SHGC syndrome affects cattle and has clinical features similar to human Seckel syndrome. Here Floriot et al. identify the causative mutation in the centrosomal protein C-Nap1 that affects centriole cohesion and cell migration, extending the range of loci involved in human Seckel-like syndromes.

Understanding factors that impact CAR T cell expansion in the clinic is crucial to improving its therapeutic success. Here the authors document heterogeneity in the clonal dynamics of CAR-T cells by tracking individual clones using the endogenous TCR and integration sites and provide further insights into the role of transcriptional states in clonal kinetics.

Genomic analysis of Plasmodium DNA from 36 ancient individuals provides insight into the global distribution and spread of malaria-causing species during around 5,500 years of human history.

The protein gephyrin is involved in organizing synapses. Here, the authors show how different transcripts of gephyrin form and regulate inhibitory synapses.

The frameshift stimulation element (FSE) of coronaviruses is an RNA structure that is required for balanced expression of viral proteins and is thus a promising drug target. A structure of the SARS-CoV-2 FSE serves as a guide for the development of antisense oligonucleotides that impair virus replication.

Cryo-electron microscopy structures of the HER2–HER3–NRG1β complex reveal a dynamic HER2–HER3 interface and explain the mechanism for the activating HER2 cancer mutations.

Ubiquitylation of H2B is associated with transcription and regulation of chromatin structure. Here, the authors perform an unbiased screen to identify the role of chromatin modifications on ubiquitylation of H2BK120 and characterize the crosstalk between H2BK120ub and H2A modifications and variants.

Crystal structures of the Ku70/80–DNA complex with Ku binding motifs of APLF and XLF reveal distinct interaction sites and an induced conformational change in Ku80 critical for function in NHEJ repair.

Adherent cells actively probe the rigidity of their substrates. Guptaet al. show that actin cytoskeleton rheology transitions from fluid to solid with increased substrate stiffness along with an isotropic to nematic ordering, implicating the remodelling of the whole actin network in rigidity sensing.

The insulin inhibitory receptor (inceptor) is found to bind to insulin and to regulate insulin stores by directing proinsulin and insulin towards lysosomal degradation.

Chimeric antigen receptors (CAR) are a promising option for cell-based immunotherapy for cancer and other immune diseases. Here the authors develop speedingCARs, an integrated CAR design and screening platform based on modular signaling domain shuffling and single cell transcriptomic analyses, and test its potential for identifying and validating novel CAR designs.