Posttranscriptional 3’-Terminal Modifications of <em>Escherichia Coli</em> RNA Fragments Evolved for Diversity Boosting

A recently emerging area of molecular biology is focused on the regulatory potential of bacterial RNA fragments that are excised from functional transcripts and acquire an in-dependent role in cells. During processing, some fragments are subject to modifications that may expand their functional inventory. Here we introduce elongation of the 5'-terminal fragments from leucine tRNAs with random sequences as a discriminative feature protecting them from Dps-dependent secretion. By analyzing 14 E. coli datasets we observed an exclusive enrichment of modified LeuT(VPQ) tRNA fragments in intracellular transcriptomes compared to secretomes and revealed dependence of their abundance on growth medium and the presence of competing bacteria. To assess the ordinariness of this modification, we developed a computational pipeline for detecting variable RNA termini in RNA-seq data. Beyond tRNALeuT(VPQ) fragments a few types of genomic loci produced oligos with heterogeneous ends, suggesting that random non-templat elongation, though most abundant in LeuT(VPQ), is not exclusive to these fragments. Regulatory potency of LeuT(VPQ) synthetic analogs tested ex vivo revealed predominantly their stimulatory ef-fect on persistence of multiple taxa in artificial microbiome, which was attenuated by 3'-end elongation. Terminal diversification of certain RNA fragments may, therefore, be considered as a process evolved to broaden the spectrum of regulatory molecules in the cell.