Cryptic tRNAs in chaetognath mitochondrial genomes

Area of Science:

• Marine Biology
• Genomics
• Evolutionary Biology

Background:

• Chaetognaths (arrow worms) are a small, enigmatic phylum of marine invertebrates.
• Their nuclear and mitochondrial genomes exhibit unique characteristics, some specific to the phylum.
• Previous understanding suggested limited transfer RNA (tRNA) genes in chaetognath mitogenomes, primarily one transfer RNA for methionine (trnMet).

Purpose of the Study:

• To re-evaluate the number and types of transfer RNA (tRNA) genes in available chaetognath mitogenomes.
• To investigate the potential translational activity and evolutionary implications of these tRNA genes.
• To explore the origin and templating of tRNAs within chaetognath mitochondrial genomes.

Main Methods:

• Reanalysis of five complete chaetognath mitogenomes using tRNAscan-SE and ARWEN software.
• Secondary structure prediction and sequence alignment of predicted tRNAs.
• Comparative analysis with non-chaetognath tRNAs and ribosomal RNA genes.

Main Results:

• Numerous additional tRNA genes of various types were identified in chaetognath mitogenomes, exceeding previous counts.
• The total number of tRNA genes remains lower than the 22 typically found in other invertebrates.
• Predicted error compensation mechanisms and coevolution of stop-suppressor tRNAs with overlapping genes suggest functional roles.
• Some tRNAs appear to be located in intergenic regions, partially overlapping with flanking genes, and some tRNA pairs may be templated by sense-antisense strands.
• 16S ribosomal RNA (rRNA) genes, but not 12S rRNAs, were identified as potential tRNA nurseries.

Conclusions:

• Chaetognath mitogenomes contain a greater diversity of tRNA genes than previously recognized.
• The identified tRNAs likely exhibit translational activity, with unique evolutionary adaptations.
• The 16S rRNA genes may serve as a source for novel tRNA gene formation in these organisms.