Bacterial double-stranded RNA-specific RNase III recognizes the A-form of an RNA helix with little sequence specificity. In contrast, baker @entity375 RNase III ( @entity64571 ) selectively recognizes NGNN tetraloops even when they are attached to a B-form DNA helix. To comprehend the general mechanism of RNase III substrate recognition, we mapped the @entity64571 binding signal and directly compared its substrate specificity to that of both @entity526 RNase III and @entity6739 RNase III (PacI). @entity64571 bound but did not cleave long RNA duplexes without NGNN tetraloops, whereas RNase III indiscriminately cleaved all RNA duplexes. PacI cleaved RNA duplexes with some preferences for NGNN-capped RNA stems under physiological conditions. @entity3787 radical footprints indicate that @entity64571 specifically interacts with the NGNN tetraloop and its surrounding @entity2036 . In contrast, @entity64571 interaction with GAAA-capped hairpins was weak and largely unspecific. Certain duality of substrate recognition was exhibited by PacI but not by bacterial RNase III. @entity526 RNase III recognized RNA duplexes longer than 11 bp with little specificity, and no specific features were required for cleavage. On the other hand, PacI cleaved long, but not short, RNA duplexes with little sequence specificity. PacI cleavage of RNA stems shorter than 27 bp was dependent on the presence of an UU-UC internal loop two @entity2036 upstream of the cleavage site. These observations suggest that @entity375 RNase IIIs have two recognition mechanisms, one that uses specific structural features and another that recognizes general features of the A-form RNA helix.

Evaluation of the RNA determinants for bacterial and XXXX RNase III binding and cleavage.

@entity6739 :: ('4896', 'Species') :: ['fission yeast'] @entity2036 :: ('MESH:D009711', 'Chemical') :: ['nucleotides'] @entity3787 :: ('MESH:D017665', 'Chemical') :: ['Hydroxyl'] @entity375 :: ('4932', 'Species') :: ['yeast'] @entity64571 :: ('855280(Tax:4932)', 'Gene') :: ['Rnt1p'] @entity526 :: ('562', 'Species') :: ['Escherichia coli', 'E. coli']
@entity375 :: (4932,Species) :: ['yeast']
