A long and abundant non-coding RNA in Lactobacillus salivarius

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Lactobacillus salivarius is a key member of the gut microbiota in humans and animals.
• Bacterial megaplasmids often encode functions for adaptation and metabolism.
• Sub-dominant commensals like L. salivarius may provide host benefits.

Purpose of the Study:

• To investigate the functions of a novel, highly abundant long non-coding RNA (lncRNA) encoded by the megaplasmid of L. salivarius UCC118.
• To characterize the expression and distribution of this lncRNA within L. salivarius species.
• To explore the potential impact of this lncRNA on bacterial gene expression.

Main Methods:

• RNA sequencing (RNA-seq) transcriptomic analysis of L. salivarius UCC118.
• rRNA depletion and analysis of non-coding RNA abundance.
• Comparative genomic analysis of L. salivarius strains.
• In vivo expression analysis during mouse intestinal transit.
• Transcriptome analysis of a lncRNA deletion mutant.

Main Results:

• A novel lncRNA, highly abundant (>75% of non-rRNA reads) and encoded by the megaplasmid, was identified in L. salivarius UCC118.
• This lncRNA's expression exceeded 16S rRNA, accumulated during growth, was stable, and detected during mouse intestinal transit.
• The lncRNA sequence is specific to L. salivarius, present in 34 of 45 analyzed genomes, and expressed at strain-specific levels.
• High lncRNA expression correlated with high megaplasmid copy number.
• Deletion of the lncRNA altered the expression of various genes, but its definitive function remains unidentified.

Conclusions:

• Lactobacillus salivarius harbors a unique and abundant lncRNA with distinctive expression properties.
• The lncRNA's presence and expression vary significantly among strains, linked to megaplasmid copy number.
• While its precise function is elusive, this lncRNA represents a novel area for basic and applied research in bacterial biology and host-microbe interactions.