An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch

Area of Science:

• Molecular Biology
• Virology
• Structural Biology

Background:

• Antitermination protein N is crucial for regulating gene expression in phage lambda.
• Protein N recognizes specific RNA structures called enhancer elements to mediate antitermination.
• Understanding the molecular mechanism of N-RNA interaction is key to phage-lambda lifecycle.

Purpose of the Study:

• To elucidate the structural basis of antitermination protein N recognition by RNA.
• To investigate how RNA structure is modulated by protein N binding.
• To understand the role of RNA-protein mimicry in antitermination.

Main Methods:

• Structural analysis of RNA-protein complexes.
• Mutational analysis of RNA sequences.
• Biochemical assays to assess antitermination activity.

Main Results:

• Protein N binds an arginine-rich peptide to one face of an RNA hairpin, organizing the other face for host complex binding.
• The RNA structure induced by protein N mimics a GNRA hairpin motif found in rRNA and ribozymes.
• Specific base stacking and base flipping patterns, extended by aromatic amino acid side chains, are critical for antitermination and are disrupted by inactivating mutations.

Conclusions:

• The N-RNA interaction involves mimicry of RNA assembly motifs by an RNA-protein complex.
• This mimicry facilitates the engagement of the N-protein with the host antitermination machinery.
• The study reveals a sophisticated mechanism of transcriptional regulation through structural mimicry.