In depth study of PRRC2B, a novel RNA binding protein that interacts with DAP5, a non-canonical translation initiation factor

Death Associated Protein 5 (DAP5; also named eIF4G2, NAT1) is a non-canonical translation initiation factor whose expression is essential for exit of embryonic stem cells (ESCs) from pluripotency towards differentiation. Several gaps still exist in understanding its various biochemical modes of action, as it forms different translation initiation complexes comprising multiple proteins. PRRC2B, an intrinsically disordered RNA binding protein, is among the strongest DAP5 interacting proteins. We identified two isoforms of PRRC2B proteins, expressed from alternatively spliced mRNA transcripts in several cell lines, including the hESCs. Pulling down each of the two isoforms revealed high degree of overlap with the cohort of DAP5 interacting proteins, including binding to eIF1, eIF2 and eIF3 and several ribosomal proteins. Both isoforms are found in the 40S and 60S fractions of polysomal gradients consistent with a role in protein translation initiation that is rather selective, as the knockout of PRRC2B has no global effect on polysomal distribution. The two isoforms of PRRC2B are localized to the cytosol and translocate to stress granules upon stress induction together with DAP5. Bioinformatic analysis of the PRRC2B along evolution, and sequence comparisons to the two other family members, PRRC2A and PRRC2C, revealed a highly conserved N-terminal domain of 200 aa termed BAT2 domain, that is indispensable for the binding to DAP5 and to eIF3d. Analysis of the transcriptome of embryoid bodies generated from PRRC2B knockout hESC, provides a list of differentially expressed genes indicating a possible role in embryonic differentiation towards neural crest fate.