Related Experiment Video
Updated: Jun 11, 2025

Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics
Published on: June 23, 2022
APEX2 proximity labeling of RNA in bacteria
Hadi Yassine1,2, Jared M Schrader3, Omer Goldberger3
1Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
Abstract:
Rapid spatially controlled methods are needed to investigate RNA localization in bacterial cells. APEX2 proximity labeling was shown to be adaptable to rapid RNA labeling in eukaryotic cells, and through the fusion of APEX2 to different proteins targeted to different subcellular locations, has been useful to identify RNA localization in these cells. Therefore, we adapted APEX2 proximity labeling of RNA to bacterial cells by generating an APEX2 fusion to the RNase E gene, which is necessary and sufficient for BR-body formation. APEX2 fusion is minimally perturbative and RNA can be rapidly labeled on the sub-minute timescale with Alkyne-Phenol, outpacing the rapid speed of mRNA decay in bacteria. Alkyne-Phenol provides flexibility in the overall downstream application with copper catalyzed click-chemistry for downstream applications, such as fluorescent dye-azides or biotin-azides for purification. Altogether, APEX2 proximity labeling of RNA provides a useful method for studying RNA localization in bacteria.
Related Concept Videos
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Labeling DNA Probes
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Bacterial RNA Polymerase
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
Types of RNA
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...

