Articles in 2023

Tian et al. developed a bacterial orthogonal DNA replication system by harnessing the temperate phage GIL16 DNA replication machinery, which provides a powerful tool for continuous evolution in prokaryotic cells.

A probe for the ubiquitin-like protein Fubi led to the discovery of dual ubiquitin/Fubi C-terminal hydrolase activity in the deubiquitinase USP16 in addition to USP36, enabling structural characterization of this distinctive Ub/Ubl specificity, and revealed a synergistic role of USP16 in ribosomal protein maturation.

Synthetic cells, modular gene-expressing compartments, have shown promising applications in biology and medicine; however, more diverse tools are required for their control and communication. Now, photocaged promoters and cell-free synthesis of an acyl homoserine lactone have been used to demonstrate light-activated communication between synthetic cells and living cells.

Phage and yeast display were used to generate variable heavy single-domain antibodies that bind and allosterically inhibit ectodomain phosphatase/phosphodiesterase-1 to increase the half-life of the immune-stimulant cyclic guanosine monophosphate adenosine monophosphate (cGAMP) in tumor microenvironments.

Tao et al. reported a series of cryo-EM structures of α-synuclein fibrils in complex with amyloid dyes and imaging tracers, and identified druggable pockets in the fibrils of multiple system atrophy.

Wu, Liu, Zou et al. report an engineered hypercompact AsCas12f system, enAsCas12f, for robust and faithful genome editing in human cells. Cryo-EM study validates the engineering strategy and reveals dimerization-based substrate recognition by AsCas12f.

Wang et al. discovered that many cancer-causing fusion proteins form abnormal condensates that affect gene expression and developed a kinetics-dependent screening method called DropScan to find drugs that can dissolve the abnormal condensates to restore normal gene expression.

The secreted aminopeptidase Pseudomonas aeruginosa aminopeptidase (PaAP) is required for nutrient recycling in biofilms. Using the information from protein structure and kinetics, a potent cyclic peptide inhibitor for PaAP was designed that killed cells in late-stage biofilms.

Genetic and bioorthogonal chemistry approaches reveal cell-to-cell movement of brassinosteroid (BR) hormones via plasmodesmata in plants. In turn, BRs positively regulate callose deposition at plasmodesmata to balance its own biosynthesis.

Engineering of a focal adhesion kinase (FAK) reporter that visualizes endogenous FAK activity with dynamic spatiotemporal resolution in living cells and vertebrates reveals tension-induced polarized FAK activity in single focal adhesions during cell migration.

Seo and Kleiner developed a small-molecule-dependent RNA editing platform termed TRIBE-ID to profile RNA–protein interactions in cells with temporal control and to study substrates of the stress granule protein G3BP1 during biomolecular condensation.

Bioinformatic and chemoproteomic approaches resulted in the identification of a homolog of human dipeptidyl peptidase 4 in the gut bacterium Bacteroides thetaiotaomicron that regulates envelope integrity and community fitness.

A carbon nanotube-based sensor was developed to monitor endolysosomal acidification events in live cells and in vivo. The technology enables a spatiotemporal measurement of endolysosomal pH and real-time tracking of the dynamics of autophagy in tumors.

A chemoproteomic approach is developed that examines changes in ligand binding-induced accessibility by globally labeling reactive proteinaceous lysines, revealing the cellular targets of glycolytic intermediates.

Wang et al. developed a bisulfite-free method termed DM-Seq that leverages an unnatural enzyme–substrate pair coupled with a DNA deaminase to sequence 5-methylcytosine at base resolution in sparse DNA samples, circumventing the limitations of chemical deamination methods.

Biochemical and structural analyses reveal how tetracenomycin X inhibits bacterial translation in a context-dependent manner that relies primarily on the presence of Gln-Lys motifs in the nascent polypeptide chain.

Phosphoribosyl pyrophosphate synthetase (PRPS1), an enzyme that regulates de novo nucleotide synthesis, was found to be O-GlcNAcylated, which increases PRPS1 activity, and is associated with increased tumorigenesis and resistance to chemoradiotherapy.

Fluorescent proteins and HaloTag allow the flexible design of FRET-based biosensors with adjustable color using different fluorescent proteins or fluorophores and readout can be modified to fluorescence intensity, lifetime or bioluminescence.

Polymerase Bcs3, which allows the fermentation-free synthesis of Haemophilus influenzae type b capsule for vaccine development, adopts a basket-like shape with all six active sites facing the interior, creating a protected environment for catalysis.

Systematically culturing combinations of auxotrophic yeast mutants leads to the identification of pairs that form obligatory cross-feeding relationships, some of which are stable over time and can divide metabolic labor for biotechnological applications.