Two polypeptides of the murine signal recognition particle (SRP), SRP9
and SRP14, bind exclusively as a heterodimer to SRP RNA and their pre
sence is required for elongation arrest activity of the particle, SRP9
/14 also constitute a subunit of small cytoplasmic Alu RNPs. To identi
fy RNA-binding determinants, we assayed the dimerization and RNA-bindi
ng capacities of altered proteins in vitro. Despite the structural hom
ology of the two proteins, their requirements for dimerization differ
substantially. In SRP9, an internal fragment of 43 amino acids is suff
icient to allow dimer formation, whereas in SRP14 only few changes, su
ch as removing an internal loop region, are tolerated without affectin
g its dimerization activity. The dimerization defect of the SRP14 prot
eins is most likely explained by a reduced stability or ability to fol
d of the proteins. Interestingly, SRP RNA can engage certain dimerizat
ion-defective SRP14 proteins into stable complexes, suggesting that lo
w-affinity interactions between the RNA and SRP14 may help to overcome
the folding defect or the reduced stability of the proteins, We ident
ified two regions, one in each protein, that are essential for RNA-bin
ding. in SRP9, acidic amino acid residues in the N-terminal alpha-heli
x and the adjacent loop and, in SRP14, a flexible internal loop region
are critical for RNA-binding. In the heterodimer, the two regions are
located in close proximity, consistent with the RNA-binding region be
ing formed by both proteins.