Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin.

OBJECTIVE: Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. RESULTS: The L. agilis epitranscriptome (minus rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.

A theoretical perspective of the physical properties of different RNA modifications with respect to RNA duplexes.

Epitranscriptomic variations include >140 different RNA modifications, many of which can serve as disease biomarkers. Owing to the challenges on synthesizing modified RNA oligos, majority of earlier studies on the effects of RNA modifications to RNA duplexes focused on selected individual epitranscriptomic variation. There are also limited development on the computational modeling of RNA duplexes containing a specific epitranscriptomic variation. This study aims to theoretically estimate the physical properties of different modified ribonucleosides and compare their variations with respect to altering the molecular structure of an RNA duplex.