Structure-based search reveals hammerhead ribozymes in the human microbiome

Area of Science:

• Microbiology
• Molecular Biology
• Bioinformatics

Background:

• Deep sequencing of microbial nucleic acids reveals microbial presence and diversity.
• Metagenomic studies of mammalian viromes aid in tracing viral transmission pathways.
• High-throughput sequencing of microbiomes has identified many sequences with unknown function or origin.

Purpose of the Study:

• To estimate the distribution of functional RNAs in metagenomic datasets.
• To identify novel hammerhead ribozyme (HHR) topologies and their activities.
• To assess the utility of structure-based searches for functional RNA discovery in large datasets.

Main Methods:

• Utilized the hammerhead ribozyme (HHR) motif for structure-based searching within metagenomic data.
• Analyzed sequences from patient and untreated sewage microbiomes.
• Confirmed identified ribozymes through in vitro experiments.

Main Results:

• Discovered highly active ribozymes, including novel HHR types, capable of assuming three distinct stem terminations.
• Identified type II HHRs as the most abundant, with one exhibiting the fastest known natural cis-acting HHR activity.
• Confirmed 13 novel ribozymes in vitro, with only one showing sequence similarity to previously known HHRs.
• Found limited sequence similarity to known genes in flanking regions, except for one instance adjacent to a bacterial RadC gene.

Conclusions:

• A structure-based search for functional RNAs is a powerful method for analyzing metagenomic data.
• This approach complements traditional sequence alignment methods for microbial sequence analysis.
• The discovery of novel HHRs expands the known repertoire of functional RNAs in microbiomes.