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.
Highlights
Lactobacillus salivarius is commonly found in the gastrointestinal tract of human and animals, and has been studied in the context of beneficial effects on the host [1, 2]
We describe an unusually abundant and stable long non-coding RNA (lncRNA) that we identified by RNA sequencing (RNA-seq) analysis of L. salivarius UCC118
RNA-seq transcriptome analysis of L. salivarius UCC118 was performed in triplicate (Fig. S2a), and a total of almost 42 billion reads were aligned to the L. salivarius UCC118 genome (Fig. S2b)
Summary
Lactobacillus salivarius is commonly found in the gastrointestinal tract of human and animals, and has been studied in the context of beneficial effects on the host [1, 2]. Analysis of traits of interest, such as resistance to bile, production of bacteriocin and exopolysaccharide, has been facilitated by the establishment of genomic and genetic tools in strain UCC118 [3, 4]. A typical L. salivarius genome presents one chromosome, one (and rarely two) megaplasmid(s) and up to three small plasmids depending on the strain [6]. The megaplasmid seems indispensable for the viability of L. salivarius, and presents strain-specific characteristics, including size and coding repertoire [4, 6]. The megaplasmid pMP118 in strain UCC118 harbours genes playing roles in environmental adaptation. The presence of this megaplasmid may explain the relatively small
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