Grad-seq

Grad-seq profiles global RNA and protein sedimentation to identify RNA–protein complexes and RNA-binding proteins in Enterococcus faecalis V583 and Enterococcus faecium AUS0004, enabling discovery of sRNA, tRNA, and untranslated region interactions and validation of conserved complexes such as the 6S RNA–RNA polymerase complex.

Key Features:

• Comprehensive Interaction Mapping: Generates global RNA and protein sedimentation profiles to identify RNA–protein complexes.
• Identification of Known and Novel Interactions: Detects both established complexes and previously uncharacterized RNA–protein associations.
• Validation of Established Complexes: Confirms conserved interactions such as the 6S RNA–RNA polymerase complex in enterococci.
• Novel Interaction Prediction: Predicts interactions involving the protein KhpB with sRNAs, tRNAs, and untranslated regions of mRNAs and suggests roles in tRNA processing.
• Strain-specific Analysis: Applies analyses specifically to Enterococcus faecalis V583 and Enterococcus faecium AUS0004.
• Detection of Regulatory RNAs: Identifies small regulatory RNAs (sRNAs) implicated in post-transcriptional gene regulation.

Scientific Applications:

• Interactome Mapping: Mapping the RNA–protein interactome of enterococci to elucidate cellular ribonucleoprotein complexes.
• Post-transcriptional Regulation Studies: Investigating sRNA-mediated regulation and untranslated region interactions that affect gene expression.
• tRNA Biology and Processing: Studying tRNA interactions and potential tRNA-processing roles of proteins such as KhpB.
• Conservation of Transcriptional Regulation: Validating conserved regulatory complexes like 6S RNA–RNA polymerase across enterococcal species.
• Functional Discovery in Gram-positive Pathogens: Supporting functional annotation and mechanistic studies relevant to antibiotic resistance and pathogenicity.

Methodology:

Uses the Grad-seq technique by analyzing global RNA and protein sedimentation profiles to predict and identify RNA–protein complexes and interactions.