Expansion of the tmRNA sequence database and new tools for search and visualization

Area of Science:

• Microbiology
• Molecular Biology
• Bioinformatics

Background:

• Transfer-messenger RNA (tmRNA) is crucial for bacterial ribosome quality control via trans-translation.
• tmRNA genes serve as integration sites for genomic islands, making their accurate identification important.
• Existing automated tools require manual validation for tmRNA gene identification.

Purpose of the Study:

• To significantly expand the database of precisely mapped tmRNA sequences.
• To develop improved methods for tmRNA gene identification and analysis.
• To investigate the integration patterns of group I introns within tmRNA genes.

Main Methods:

• Compiled and curated an extensive database of unique tmRNA sequences, increasing its size over 50-fold.
• Analyzed the distribution and integration sites of group I introns within tmRNA genes.
• Developed new covariance models and secondary structure visualization tools for tmRNA analysis.

Main Results:

• The tmRNA sequence database now contains 97,179 unique sequences.
• Group I introns were identified at four distinct subsites within the TψC-loop of tmRNA genes, indicating multiple invasion events.
• tmRNA genes were detected in metagenomic archaeal genomes, likely due to sequence misbinning.

Conclusions:

• The expanded tmRNA database and new analytical tools enhance the accuracy of tmRNA gene identification.
• Findings suggest multiple independent invasions of tmRNA genes by group I introns.
• The presence of tmRNA genes in archaeal genomes warrants further investigation into horizontal gene transfer or assembly artifacts.