The role of codY in streptococcus thermphilus
Total RNA isolation of S. thermophilus ST2017 and S. thermophilus ST2017ΔcodY was carried out according to the manufacturer’s instructions (Total RNA Kit Midi Kit Omega, USA). To remove rRNA, Ribo-Zero rRNA Removal Kit (epicenter, Madison, USA) was applied according to manufacturers’ instructions. The mRNA was fragmented ultrasonically and fragmented mRNA with a length of 200–300 bp were converted into a RNA-seq library using the mRNA-seq library construction kit (Illumina Inc., San Diego, CA, USA). RNA sequencing was performed on a Illumina Hiseq2000 (Illumina, San Diego, CA, USA) platform. Clean reads were achieved from the raw reads by filtering dirty reads which contained adapters, low quality or unknown bases, and were imported into DEGseq. Then, the MARS model in the DEGseq package was used to calculate the expression abundance of each gene between S. thermophilus ST2017 and S. thermophilus ST2017ΔcodY. False discovery rate (FDR) was used to determine the threshold of the p value. We identified differentially expressed genes as those that were significant at FDR < 0.001 and Normalized Fold_change≥2.