A long and abundant non-coding RNA in Lactobacillus salivarius

Abstract

Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq)transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L . salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.

Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus

“…Noncoding RNAs participate in gene expression regulation ( 28 ), but it has also been difficult to ascertain function for the phage lncRNAs and sncRNAs in previous studies ( 23 , 24 , 29 ). Two lncRNAs in phage K genome resemble GOLLD and ROOL ribozymes from Lactobacillus prophages ( 30 , 31 ) by their location relative to tRNA genes and by their abundant transcription. The role of the phage K lncRNAs could be also related to bacterial survival under stress conditions, as described in extremophilic bacteria OLE RNA ( 32 ), or may be linked to the phage genome copy number, which is the case for lncRNA expressed from a Lactobacillus salivarius megaplasmid ( 31 ).…”

Interactions between the MicroRNAs and Microbiota in Cancer Development: Roles and Therapeutic Opportunities

“…An RNA sequencing transcriptomic study of the L. salivarius strain UCC118 recognised the presence of an uncommonly abundant lncRNA encoded by the megaplasmid [88].…”

Transcriptional Landscapes of Herelleviridae Bacteriophages and Staphylococcus aureus during Phage Infection: An Overview

“…These RNAs exhibited similarities in terms of their position relative to tRNA genes and their transcription levels. Interestingly, these RNAs exhibit similarities in terms of their sequences to the ribozymes GOLLD and ROOL found in Lactobacillus prophages [ 67 , 68 ]. It is postulated that the potential role of lncRNAs may be linked to the survival of bacteria under stressful conditions, as exemplified by the RNA OLE in extremophilic bacteria [ 69 ].…”

“…It is postulated that the potential role of lncRNAs may be linked to the survival of bacteria under stressful conditions, as exemplified by the RNA OLE in extremophilic bacteria [ 69 ]. Additionally, lncRNAs may play a role in regulating the copy number of the phage genome, as observed in the case of lncRNA expression from the megaplasmid of Lactobacillus salivarius [ 68 ]. Conversely, only phage K has been investigated in terms of sncRNAs and their potential interactions with bacterial targets.…”