Products of abortive transcription can prime synthesis of chimeric oligonucleotides

K. S. Shavkunov ; N. Yu. Markelova ; O. V. Alikina ; O. A. Glazunova ; V. V. Panyukov ; N. P. Kolzhetsov ; S. S. Kiselev ; O. N. Ozoline

Matematičeskaâ biologiâ i bioinformatika, Tome 19 (2024) no. 2, pp. 453-471.

Résumé

The aim of the study was to search for signal RNAs potentially utilized by bacteria for intercellular interactions. This was not limited to a certain category of regulatory RNAs, which are contained in large numbers in all domains of life. The search was performed using RNA-seq data obtained for a wild-type strain of E. coli and its mutant derivative $(\Delta dps)$ lacking the gene encoding nucleoid protein Dps. This protein can bind RNAs and is found in membrane structures, which indicates the possibility of its participation in their secretion. Since the spectra of intracellular and secreted RNAs differed, it was assumed that the secreted RNAs are somehow selected for secretion. Therefore, in the RNA sets with Dps-dependent secretion, we searched for and found reads with non-template nucleotides at the ends, point nucleotide substitutions, insertions and deletions, as well as regularly detected chimeras. One chimera with a 9-mer GCCAAGGCG at the 5'-end and a transcript from the fimA-fimI intergenic region at the 3'-end was chosen for detailed study. It was found that the 9-mer is a product of abortive transcription from the antisense promoter inside the ravA gene. It is efficiently secreted and forms chimeras with many RNAs, including their 5'-ends and fragments shortened from this terminus. Analysis of the 5'-ends of the 9-mer partners in different chimeras revealed their coding sites in the genome, a feature of which was the ability to form stable secondary structures and therefore cause transcription stops or pauses. The discovery of different chimeras with the 9-mer at the 5'-end witnesses that they are formed as a result of primed synthesis rather than random ligation. The possible biological role of transcription primed by abortive products, whose regulatory role has been established for the first time, is discussed.