Protocol to identify E3 ligases amenable to biodegraders using a cell-based screening.

Here, we provide a protocol for the identification of E3 ubiquitin ligases that are functional when implemented as biodegraders using a cell-based screening assay. We describe steps for establishing a stable cell line expressing a GFP-tagged protein of interest (POI), preparing a sub-library of E3 ligases to screen, and performing the cell-based screening. This protocol can be broadly applied to identify any functional E3 ligase in a biodegrader setting.

Cytidine deaminase-dependent mitochondrial biogenesis as a potential vulnerability in pancreatic cancer cells.

Cytidine deaminase (CDA) converts cytidine and deoxycytidine into uridine and deoxyuridine as part of the pyrimidine salvage pathway. Elevated levels of CDA are found in pancreatic tumors and associated with chemoresistance. Recent evidence suggests that CDA has additional functions in cancer cell biology.

isolateR: an R package for generating microbial libraries from Sanger sequencing data.

Motivation: Sanger sequencing of taxonomic marker genes (e.g. 16S/18S/ITS/rpoB/cpn60) represents the leading method for identifying a wide range of microorganisms including bacteria, archaea, and fungi.

Discovery of SOCS7 as a versatile E3 ligase for protein-based degraders.

Targeted protein degradation (TPD) strategy harnesses the ubiquitin-proteasome system (UPS) to degrade a protein of interest (POI) by bringing it into proximity with an E3 ubiquitin ligase. However, the limited availability of functional E3 ligases and the emergence of resistance through mutations in UPS components restrict this approach. Therefore, identifying alternative E3 ligases suitable for TPD is important to develop new degraders and overcome potential resistance mechanisms.

Fiber-deficient diets reprogram the microbiota.

Exclusive enteral nutrition, a diet lacking fiber, is used to treat pediatric Crohn's disease. In this issue of Cell Host & Microbe, Kuffa et al. find that a fiber-deficient diet thins the mucus layer and alters microbial cross-feeding, causing pro-inflammatory Mucispirillum to move away from the epithelium, which ameliorates colitis.