A sequence predicted to form a stem-loop is proposed to be required for formation of an RNA-protein complex involving the 3'UTR of β-subunit F0F1-ATPase mRNA

ATP-synthase assembly requires coordinated control of ATP mRNA translation; this may e.g. occur through the formation of mRNA-protein complexes. In this study we aim to identify sequences in the 3'UTR of the β-subunit F1-ATPase mRNA necessary for RNA-protein complex formation. We examined the interaction between a brain cytoplasmic protein extract and in vitro-synthesized β-subunit 3'UTR probes containing successive accumulative 5'- and 3'-deletions, as well as single subregion deletions, with or without poly(A) tail. Using electrophoretic mobility shift assays we found that two major RNA-protein complexes (here called RPC1 and RPC2) were formed with the full-length 3'UTR. The RPC2 complex formation was fully dependent on the presence of both the poly(A) tail and one subregion directly adjacent to it. For RPC1 complex formation, a 3'UTR sequence stretch (experimentally divided into three subregions) adjacent to but not including the poly(A) tail was necessary. This sequence stretch includes a conserved 40-nucleotide region that, according to the structure prediction program mfold, is able to fold into a characteristic stem-loop structure. Since the formation of the RPC1 complex was not dependent on a conventional sequence motif in the 3'UTR of the β-subunit mRNA but rather on the presence of the predicted stem-loop-forming region as such, we hypothetize that this RNA region, by forming a stem-loop in the 3'UTR β-subunit mRNA, is necessary for formation of the RNA-protein complex.