Selective recognition of PTRE1 transcripts mediated by protein–protein interaction between the m⁶A reader ECT2 and PTRE1

N⁶-methyladenosine (m⁶A) is a prevalent internal post-transcriptional modification in eukaryotic RNAs executed by m⁶A-binding proteins known as “readers.” Our previous research demonstrated that the Arabidopsis m⁶A reader ECT2 positively regulates transcript levels of the proteasome regulator PTRE1 and several 20S proteasome subunits, thereby enhancing 26S proteasome activity. However, mechanism underlying the selective recognition of m⁶A targets by readers, such as ECT2, remains elusive. In this study, we further demonstrate that ECT2 physically interacts with PTRE1 and several 20S proteasome subunits. This interaction, which occurs on the ribosome, involves the N terminus of PTRE1, suggesting that ECT2 might bind to the nascent PTRE1 polypeptide. Deleting ECT2’s protein interaction domain impairs its mRNA-binding ability, whereas mutations in the m⁶A-RNA-binding site do not affect protein–protein interactions. Moreover, introducing a novel protein-binding domain into ECT2 increases transcript levels of proteins interacting with this domain. Our findings indicate that interaction with the PTRE1 protein enhances ECT2’s binding to PTRE1 m⁶A mRNAs during translation, thereby regulating PTRE1 mRNA levels.