Sense overlapping transcripts in IS 1341-type transposase genes are functional non-coding RNAs in archaea

The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS<i>1341</i>-type transposase (<i>tnpB</i>) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon <i>Halobacterium salinarum</i> NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS<i>1341</i>-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a <i>H. salinarum</i> intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved <i>H. salinarum</i> growth, indicating that these ncRNAs are functional.