Citation
- Authors: Gourdomichali O. et al.
- Year: 2022
- Journal: Biology 11 287
- Applications: in vitro / DNA / jetOPTIMUS
- Cell type: SK-N-SH
Description: Human bone marrow neuroblastoma
Method
Neuroblastoma SK-N-SH and HEK-293 cells were grown in high-glucose DMEM + 10% FBS and 1% p/s. Cells were kept at 37 °C in a humidified 5% CO2 incubator. SK-N-SH cells were transfected at the time of plating with APEX2 alone or TIA1-APEX2 hybrid expression plasmids by using the JetOptimus reagent (Polyplus).
Thirty-six hours after transfection, cells were incubated in 1 mM biotin tyramide and 330 μM NaAsO2 (reduced to 100 μΜ when used for immunofluorescence staining due to the cells’ poor adhesion at higher concentrations), where appropriate, for 45 min at 37 °C. After that, H2O2 was added at a final concentration of 1 mM for exactly 1.5 min at RT. The reaction was quenched by adding Trolox and sodium ascorbate dissolved in PBS to a final concentration of 5 mM and 10 mM, respectively.
Abstract
TIA1 is a broadly expressed DNA/RNA binding protein that regulates multiple aspects of RNA metabolism. It is best known for its role in stress granule assembly during the cellular stress response. Three RNA recognition motifs mediate TIA1 functions along with a prion-like domain that supports multivalent protein-protein interactions that are yet poorly characterized. Here, by fusing the enhanced ascorbate peroxidase 2 (APEX2) biotin-labeling enzyme to TIA1 combined with mass spectrometry, the proteins in the immediate vicinity of TIA1 were defined in situ. Eighty-six and 203 protein partners, mostly associated with ribonucleoprotein complexes, were identified in unstressed control and acute stress conditions, respectively. Remarkably, the repertoire of TIA1 protein partners was highly dissimilar between the two cellular states. Under unstressed control conditions, the biological processes associated with the TIA1 interactome were enriched for cytosolic ontologies related to mRNA metabolism, such as translation initiation, nucleocytoplasmic transport, and RNA catabolism, while the protein identities were primarily represented by RNA binding proteins, ribosomal subunits, and eicosanoid regulators. Under acute stress, TIA1-labeled partners displayed a broader subcellular distribution that included the chromosomes and mitochondria. The enriched biological processes included splicing, translation, and protein synthesis regulation, while the molecular function of the proteins was enriched for RNA binding activity, ribosomal subunits, DNA double-strand break repair, and amide metabolism. Altogether, these data highlight the TIA1 spatial environment with its different partners in diverse cellular states and pave the way to dissect TIA1 role in these processes.