RNA recognition by minimal ProQ fromNeisseria meningitidis

Abstract

ABSTRACTNeisseria meningitidisminimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. TheN. meningitidisProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs,rpmG-3’ and AniS, were subject to further mutational studies. The data showed thatN. meningitidisProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5’ and 3ʹ side of terminator stem are required for tight binding. However, the specific lengths of 5’ and 3ʹ RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2ʹ-OH and 3ʹ-OH groups of the 3ʹ terminal ribose contribute to RNA binding byN. meningitidisProQ. In summary, the minimal ProQ protein fromN. meningitidishas generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.