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| Volume 20 Issue 2 Year 2025 | ||
Intramolecular "Chimerization" of Escherichia coli RNAs as a New Type of Transcript Editing
Shvyreva U.S.1, Boyko L.E.2, Kolzhetsov N.P.1, Shavkunov K.S.1, Glazunova O.A.1, Alikina O.V.1, Markelova N.Yu.1, Panyukov V.V.3,1, Ozoline O.N.1 1Institute of Cell Biophysics, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia Abstract. Chimeric RNAs, composed of sequences from different genes, are the least studied category of bacterial RNAs, and their very existence has not been universally recognized so far. The primary aim of this study was to test the hypothesis that unusual RNA chimeras can arise from transcription priming by a specific 8/9-nucleotide RNAs, GCCAAGGC(G). Applying single-molecule sequencing of Escherichia coli cDNA on Oxford Nanopore MinIon platform, we confirmed the expected presence of these 8/9-mers at the 5'-ends of numerous transcripts. Surprisingly, we also discovered thousands of transcripts from diverse genes containing an internal insertion of the GCCAAGGC 8-mer as a replacement of native genomic 3-15 nucleotide sequences. Given that only 1.52 ± 0.47 % of oligonucleotides, containing this 8-mer as a genomic sequence, carry a single-nucleotide substitution within it, the revealed intramolecular “chimeras” likely represent genuine post-transcriptional RNA modifications not compromised by potential artifacts of the experiment. Notably, the substitutions occurred predominantly at sites where the replaced genomic sequences contained GC dinucleotides at both borders. We detected no consensus sequences in the 20-nucleotide flanks near the modification site, implying that signals for intramolecular modifications are located within the replaceable segments. Although detected in over two hundred distinct gene products, most of the chimeric transcripts originated from 16S or 23S rRNAs and were often located within antisense transcripts. The discovered modification has no analogues. While this article discusses its possible biological role, further investigation will require new approaches and fresh conceptual ideas.
Key words: chimerization of bacterial RNAs, post-transcriptional RNA editing, bacterial secreted RNAs, antisense RNAs, nanopore transcriptomics |
Table of Contents
Original Article
Shvyreva U.S., Boyko L.E., Kolzhetsov N.P., Shavkunov K.S., Glazunova O.A., Alikina O.V., Markelova N.Yu., Panyukov V.V., Ozoline O.N. Intramolecular "Chimerization" of Escherichia coli RNAs as a New Type of Transcript Editing. Ìàthematical biology and bioinformatics. 2025;20(2):653-666. doi: 10.17537/2025.20.653 (published in English) Abstract (eng.) Abstract (rus.) Full text (eng., pdf) References
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