A Modular RNA Domain That Confers Differential Ligand Specificity

Area of Science:

• Molecular Biology
• Biochemistry
• RNA Structure and Function

Background:

• Protein domain modularity is well-established.
• RNA domain modularity for ligand binding is less understood.
• The ykkC RNA aptamer family binds diverse ligands like guanidine, phosphoribosyl pyrophosphate (PRPP), and guanosine tetraphosphate (ppGpp).

Purpose of the Study:

• To investigate the modularity of RNA aptamer domains.
• To determine if specific helical regions within ykkC aptamers dictate ligand specificity.
• To explore the potential for RNA molecular evolution through domain adaptation.

Main Methods:

• Structural analysis of ykkC aptamers revealed two coaxial helical stacks.
• Experimental swapping of ligand-binding coaxial stacks between guanidine and PRPP aptamers.
• Introduction of a single mutation in the scaffold domain to assess specificity changes.

Main Results:

• Swapping ligand-binding helices successfully switched the ligand specificity of the aptamers.
• A single mutation in the scaffold domain contributed to the specificity switch.
• The ligand-binding helix was identified as the primary determinant of ykkC RNA ligand specificity.

Conclusions:

• ykkC RNA aptamers exhibit domain modularity analogous to protein domains.
• The scaffold coaxial stack is adaptable to different ligand-binding modules.
• This study highlights RNA's versatility and potential for molecular evolution via motif adaptation.