Subject(s)
Chaperonin Containing TCP-1 , Eukaryotic Initiation Factor-3 , Protein Folding , Chaperonin Containing TCP-1/metabolism , Chaperonin Containing TCP-1/genetics , Eukaryotic Initiation Factor-3/metabolism , Eukaryotic Initiation Factor-3/genetics , Eukaryotic Initiation Factor-3/chemistry , Humans , Protein Subunits/metabolism , Protein Subunits/genetics , Protein Subunits/chemistry , Protein BindingABSTRACT
Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, showcasing how this approach can reveal the function of uncharacterised proteins and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
Subject(s)
Escherichia coli Proteins , Escherichia coli , RNA, Bacterial , RNA-Binding Proteins , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Escherichia coli/growth & development , Escherichia coli/metabolism , Escherichia coli/genetics , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/genetics , RNA, Bacterial/metabolism , RNA, Bacterial/genetics , Proteome/metabolism , Protein Binding , Gene Expression Regulation, Bacterial , HumansABSTRACT
Molecular chaperones are critical for protein homeostasis and are implicated in several human pathologies such as neurodegeneration and cancer. While the binding of chaperones to nascent and misfolded proteins has been studied in great detail, the direct interaction between chaperones and RNA has not been systematically investigated. Here, we provide the evidence for widespread interaction between chaperones and RNA in human cells. We show that the major chaperone heat shock protein 70 (HSP70) binds to non-coding RNA transcribed by RNA polymerase III (RNA Pol III) such as tRNA and 5S rRNA. Global chromatin profiling revealed that HSP70 binds genomic sites of transcription by RNA Pol III. Detailed biochemical analyses showed that HSP70 alleviates the inhibitory effect of cognate tRNA transcript on tRNA gene transcription. Thus, our study uncovers an unexpected role of HSP70-RNA interaction in the biogenesis of a specific class of non-coding RNA with wider implications in cancer therapeutics.
Subject(s)
HSP70 Heat-Shock Proteins , Neoplasms , Humans , HSP70 Heat-Shock Proteins/genetics , HSP70 Heat-Shock Proteins/metabolism , Molecular Chaperones/metabolism , RNA , RNA Polymerase III/genetics , RNA Polymerase III/metabolism , RNA, Transfer/genetics , RNA, Untranslated/geneticsABSTRACT
EIF4A1 and cofactors EIF4B and EIF4H have been well characterised in cancers, including B cell malignancies, for their ability to promote the translation of oncogenes with structured 5' untranslated regions. However, very little is known of their roles in nonmalignant cells. Using mouse models to delete Eif4a1, Eif4b or Eif4h in B cells, we show that EIF4A1, but not EIF4B or EIF4H, is essential for B cell development and the germinal centre response. After B cell activation in vitro, EIF4A1 facilitates an increased rate of protein synthesis, MYC expression, and expression of cell cycle regulators. However, EIF4A1-deficient cells remain viable, whereas inhibition of EIF4A1 and EIF4A2 by Hippuristanol treatment induces cell death.