Widespread occurrence of self-cleaving ribozymes

Area of Science:

• Molecular Biology
• RNA Biology
• Genomics

Background:

• Hepatitis delta virus (HDV) and cytoplasmic polyadenylation element-binding protein 3 (CPEB3) ribozymes are self-cleaving RNAs.
• They share a conserved nested double-pseudoknot structure with minimal sequence conservation.

Purpose of the Study:

• To identify novel sequences forming the HDV-like ribozyme fold.
• To investigate the distribution and biological activity of these ribozymes in nature.

Main Methods:

• Secondary structure-based computational searches were employed to identify potential ribozyme sequences.
• In vitro assays were used to confirm the self-cleavage activity of identified sequences.
• Sequence homology searches were conducted to expand the discovery across various taxa.

Main Results:

• Active HDV-like ribozymes were discovered in marine organisms, nematodes, arthropods, bacteria, and insect viruses.
• These ribozymes were also found in plants, fungi, and a unicellular eukaryote.
• Differential expression and self-cleavage activity were observed in Anopheles gambiae during early developmental stages.

Conclusions:

• HDV-like ribozymes are widely distributed throughout nature.
• The abundance and varied expression of these self-cleaving RNAs suggest diverse and important biological roles.