From genetic to structural characterization of a new class of RNA-binding domain within the SacY/BglG family of antiterminator proteins

Abstract

SacY is the prototype of a family of regulatory proteins able to prevent transcription termination. It interacts with a 29 nucleotide RNA sequence able to fold into a stem–loop structure and partially overlapping with a terminator sequence located in the 5′ leader mRNA region of the gene it controls. We show here that the N‐terminal fragment of SacY, SacY(1–55), and the corresponding fragments of other members of the family have antiterminator activities with efficiency and specificity identical to those of the full‐length proteins. In vitro, this activity correlates with the specific affinity of SacY(1–55) for its RNA target. UV melting experiments demonstrate that SacY(1–55) binding stabilizes the RNA target structure. The NMR solution structure of SacY(1–55) is very similar to that obtained in the crystal (van Tilbeurgh et al., 1997): the peptide is folded as a symmetrical dimer without any structural homology with other RNA‐binding domains yet characterized. According to a preliminary NMR analysis of the SacY(1–55)–RNA complex, the protein dimer is not disrupted upon RNA binding and several residues implicated in RNA recognition are located at the edge of the dimer interface. This suggests a new mode of protein–RNA interaction.