The kink-turn: a new RNA secondary structure motif

Area of Science:

• Structural Biology
• Molecular Biology
• RNA Biology

Background:

• Ribosomal RNA (rRNA) and other non-coding RNAs fold into complex three-dimensional structures essential for their function.
• Identifying conserved structural motifs is crucial for understanding RNA-protein interactions and RNA function across different species.

Purpose of the Study:

• To identify and characterize a common RNA structural motif within the large ribosomal subunit of Haloarcula marismortui.
• To determine the prevalence and structural features of this motif in other RNA molecules and its potential role in RNA-protein interactions.

Main Methods:

• High-resolution structural analysis of Haloarcula marismortui 23S rRNA.
• Comparative structural analysis of rRNA and other RNA molecules (e.g., 16S rRNA, U4 snRNA, mRNA fragments).
• Secondary structure prediction and analysis.

Main Results:

• A conserved RNA structure, termed the kink-turn (K-turn), was identified in H. marismortui 23S rRNA, characterized by a kink in the phosphodiester backbone and a sharp helical turn.
• The K-turn motif was found in other RNA molecules, including Thermus thermophilus 16S rRNA, U4 snRNA, and L30e mRNA fragments.
• A consensus secondary structure for the K-turn was derived, predicting its presence in various other RNAs like L10 mRNA and Escherichia coli 23S rRNA.
• Five K-turns in 23S rRNA interact with nine proteins, showing specific interactions with L7Ae and homologous proteins.

Conclusions:

• The kink-turn (K-turn) is a prevalent and conserved RNA structural motif with distinct geometric and sequence features.
• K-turns play a role in organizing RNA structure and mediating specific interactions with ribosomal proteins, particularly the L7Ae family.