6S RNA in lactic acid bacteria

CATALDO, P. G.

Bled

Seminario; 34th TBI Winterseminar "Computational Biology, Computational Mathematics, Theoretical Biology, Bioinformatics, Biological Networks"; 2019

Institute for Theoretical Chemistry- University of Vienna

We have succesfully employed Bioinformatic tools to identify 6S RNA sequences in a set of genomes from Lactic Acid Bacteria (LAB), being ours the first global study of this important non-coding RNA in this industrial and health relevant group of microorganisms. We have performed both sequence-and structure-based alignments of the 6S RNA sequences and also built a phylogenetic tree based on the mLOCARNA calculated distances. Sequence and structure conservation was also assessed and a consensus, canonical secondary structure was modeled. We were also able to predict putative product RNA (pRNA) sequences and their corresponding transcription starting sites based on previous works ofDr. Lechner group with Bacillus subtilis 6S RNA. We further used these sequences to find a common motif within the pRNAs and compared it to other pRNA sequences reported up to date in the literature. Furthermore, we studied the genomic architechture of the LAB genomes in the vecinity of the 6S RNA genes (synteny analysis). On the other hand, we analysed the presence of Carbon Responsive Elements both upstream and downtream of the 6S RNA and compared this results with previous reports available in the literature.From an experimental perspective, we were able to detect 6S RNA transcripts in many growth conditions in the model organism Lactobacillus brevis CRL 2013 by RT-qPRC assays which supports our bioinformatic work. Besides, we used deep sequencing data available in public databases to detect transciption of the 6S RNA in other 22 LAB species.