Prediction and identification of non-coding sRNAs in Corynebacterium glutamicum at different growth stages

Abstract:

[Objective] To investigate the small non-coding RNAs (sRNAs) in Corynebacterium glutamicum at different growth stages.[Methods] We examined the RNA-Seq data of C. glutamicum strains at different growth stages and transformed for industrial production and then employed sRNA-Detect and APERO approaches to construct the prospective sRNA library. real-time reverse transcription PCR (RT-PCR) was carried out to determine the expression of sRNAs. The functions, secondary structures, and conserved domains of potential sRNAs were predicted by bioinformatics tools. [Results] We constructed a library containing 2 653 potential sRNAs and performed classification and functional prediction based on their positions relative to the coding sequence (CDS) region. We identified sRNA00130 ubiquitous in Gram-positive bacteria with high GC content, sRNA00257 with varied expression during the growth period, and sRNA02036 and sRNA02037 with high expression. We predicted the possible binding sites and secondary structures of potential sRNAs based on free binding energy. The prediction results showed that potential sRNAs were associated with a variety of genes involved in cell replication and metabolic pathways. Most potential sRNAs were conserved only in C. glutamicum. [Conclusion] The discovery of potential sRNAs in C. glutamicum helps to fill the vacancy in the growth regulation mechanism of C. glutamicum and provides a new possible regulation tool and modification site.

Key words:Corynebacterium glutamicum;small non-coding RNAs (sRNA);bioinformatics;genome-wide analysis;sRNA-Detect