Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
- Humboldt University Berlin, Germany
Abstract
The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.
Data availability
The RNA and DNA sequencing data generated in this study have been submitted to the NCBI BioProject database https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA978626. New block annotations can be found in GenBank, OR086910 - OR086916.
Article and author information
Author details
Christian Schmitz-Linneweber
Funding
Deutsche Forschungsgemeinschaft (IRTG2290-B01)
- Christian Schmitz-Linneweber
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Marisa Nicolás, Laboratório Nacional de Computação Científica, Brazil
Version history
- Preprint posted: September 2, 2023 (view preprint)
- Received: December 29, 2023
- Accepted: January 23, 2024
- Accepted Manuscript published: February 16, 2024 (version 1)
- Version of Record published: March 18, 2024 (version 2)
Copyright
© 2024, Tetzlaff et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
eLife 13:e95407.
https://doi.org/10.7554/eLife.95407
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