The structural basis of RNA-catalyzed RNA polymerization

Area of Science:

• Biochemistry
• Molecular Biology
• Astrobiology

Background:

• Early life likely depended on self-replicating RNA molecules.
• RNA ligase ribozymes, selected from random sequences, are key candidates for ancient RNA replicases.

Purpose of the Study:

• To elucidate the catalytic mechanism of an RNA ligase ribozyme, a potential RNA polymerase.
• To understand the structural basis of RNA replication by artificial ribozymes.

Main Methods:

• Obtained high-resolution (3.15 Å) crystal structures of the ribozyme in catalytically relevant preligation states.
• Utilized atomic mutagenesis experiments to probe the roles of active site residues in catalysis.

Main Results:

• Captured the ribozyme with the 3'-hydroxyl nucleophile poised for attack on the 5'-triphosphate.
• Revealed an unexpected RNA-metal-solvent coordination network guiding substrate binding.
• Identified direct participation of nucleobase and hydroxyl groups in catalysis, mimicking a second metal ion's role in protein polymerases.

Conclusions:

• Artificial ribozymes employ complex catalytic strategies distinct from protein enzymes.
• Structural insights provide a mechanistic understanding of RNA replication by ribozymes.
• This work sheds light on the potential of RNA in early life biochemistry.