Project description:Quantitative proteomic analysis raw data for the manuscript entitled “A covalent peptide-based lysosome-targeting protein degradation platform for cancer immunotherapy”.
Project description:Protein synthesis is a major energy-consuming process of the cell, which requires controlled production and turnover of ribosomes. While the last years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3’ to 5’ exonuclease, RNase R. The structures reveal that RNase R binds initially to the 30S platform to facilitate degradation of the functionally important anti-Shine-Dalgarno sequence and decoding site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S, which is overcome by a major structural rearrangement of the 30S head, involving loss of ribosomal proteins. RNase R parallels this movement, relocating to the decoding site, by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also that the enzyme alone is sufficient for complete 30S degradation. Collectively, our results provide a mechanistic basis for RNase R-mediated 30S degradation and reveal that RNase R targets orphaned 30S subunits using a dynamic anchored binding site switching mechanism.
Project description:We used HSUR1 – a small non-coding RNA from Herpesvirus saimiri that induces degradation of host miR-27 – to validate structural insights into target-directed miRNA degradation (TDMD). While performing systematic mutagenesis of HSUR1 we noticed that HSUR1 mutants exhibiting complementarity to the extreme 3' end of miR-27, lead to generation of extended miR-27 isoforms (isomiRs). These isomiRs likely represent failed products of TDMD and could mean that features of the pairing between the TDMD target and miRNA dictate which enzymes are recruited to modify the miRNA 3′ end. Small RNA sequencing revealed that a mixture of adenylates and uridylates is added to the 3′ end of miR-27 during TDMD.
Project description:Lysosome-mediated degradation of extracellular proteins represents an emerging therapeutic paradigm that exploits cellular waste-disposal machinery to eliminate pathogenic targets. Despite its promise, achieving selective degradation of disease-associated proteins remains constrained by the scarcity of discovering highly effective disease-specific lysosome-targeting receptors. To address this limitation, we engineered NeuroTAC, a lysosome-targeting chimera (LYTAC) that bridges a sortilin-binding ligand-neurotensin (NT) to a disease-specific antibody targeting proteins overexpressed in tumors and inflammatory disorders. NeuroTAC demonstrated robust degradation efficacy against both membrane-bound and extracellular proteins in experimental models. Leveraging the dysregulated activity of matrix metalloproteinases (MMPs), a characteristic feature of tumor and inflammatory microenvironments, we further developed BioresTAC as an innovative bioresponsive LYTAC variant. This advanced construct integrates an MMP-cleavable linker and terminal RGD peptides, enabling MMP-triggered activation and spatial precision in MMP-enriched pathological niches. Systematic validation demonstrated that NeuroTAC and BioresTAC mediate broad-spectrum protein degradation with microenvironmental selectivity, enhancing therapeutic efficacy in cancer and psoriasis models. These findings advance the translational potential of lysosome-engaging biologics, offering a dual strategy for precision degradation through receptor recruitment and microenvironmental sensing.
Project description:This SuperSeries is composed of the following subset Series: GSE17162: Structural and Functional Analysis of Viral siRNAs using Solexa sequencing GSE17164: Structural and Functional Analysis of Viral siRNAs using 454 sequencing Refer to individual Series
Project description:Post-transcriptional processing and modification of messenger RNA (mRNA) regulates gene expression in eukaryotes by dictating the stability, localisation and translation of newly synthesised transcripts 1. These epitranscriptomic events are coordinated by an extensive network of RNA-binding proteins 2,3. Here we observed that the bacterial pathogen, Legionella pneumophila, caused the selective degradation of host cellular mRNAs encoding factors involved in glycolysis and related metabolic pathways. Screening of a library of L. pneumophila deletion mutant strains revealed a single effector protein, LegC4, that mediated the post-transcriptional degradation of host mRNAs encoding key glycolytic enzymes, thereby suppressing host glycolysis during infection. Using CLIP-seq and complementary methods, we observed that LegC4 bound to mature processed host mRNA recognising a guanine (G)-rich motif that was overrepresented within mRNAs targeted for degradation. In vitro activity assays showed that LegC4 harboured intrinsic RNase activity and structural determination of a catalytically inactive mutant of LegC4 in complex with single-stranded RNA revealed a unique RNA-binding domain 4. The selective binding and degradation of host mRNA by LegC4 reveals a previously undescribed mechanism of bacterial effector protein activity targeting the host epitranscriptome.
Project description:BioresTAC introduces microenvironment-responsive activation: its protease-triggered design exploits dysregulated enzymes in tumors and inflamed tissues to restrict degradation activity to pathological niches. Preclinical validation in cancer and psoriasis models demonstrates enhanced efficacy with reduced off-target effects, establishing a dual-action paradigm—receptor-driven targeting and context-dependent activation—that redefines precision medicine for protein degradation therapies.
Project description:Quantitative proteomic analysis raw data for the manuscript entitled “Chemically Engineered Antibodies for Autophagy-based Receptor Degradation”.