Abstract
Small regulatory RNA (sRNA) has been shown to play an important role under various stress conditions in bacteria, and it plays a vital role in regulating growth, adaptation and survival through posttranscriptional control of gene expression in bacterial cells. Streptococcus thermophilus is widely used as a starter culture in the manufacture of fermented dairy products. However, the lack of reliable information on the expression profiles and potential physiological functions of sRNAs in this species hinders our understanding of the importance of sRNAs in S. thermophilus. The present study was conducted to assess the expression profiles of sRNAs in S. thermophilus and to identify sRNAs that exhibited significant changes. A total of 530 potential sRNAs were identified, including 198 asRNAs, 135 sRNAs from intergenic regions, and 197 sRNAs from untranslated regions (UTRs). Significant changes occurred in the expression of 238, 83, 194, and 139 sRNA genes during the lag, early exponential growth, late exponential growth, and stationary phases, respectively. The expression of 14 of the identified sRNAs was verified by qRT-PCR. Predictions of the target genes of these candidate sRNAs showed that the primary metabolic pathways targeted were involved in carbon metabolism, biosynthesis of amino acids, ABC transporters, the metabolism of amino and nucleotide sugars, purine metabolism, and the phosphotransferase system. The expression of the predicted target genes was further analyzed to better understand the roles of sRNAs during different growth stages. The results suggested that these sRNAs play crucial roles by regulating biological pathways during different growth phases of S. thermophilus. According to the results, sRNAs sts141, sts392, sts318, and sts014 are involved in the regulation of osmotic stress. sRNAs sts508, sts087, sts372, sts141, sts375, and sts119 are involved in the regulation of starvation stress. sRNAs sts129, sts226, sts166, sts231, sts204, sts145, and sts236 are involved in arginine synthesis. sRNAs sts033, sts341, sts492, sts140, sts230, sts172, and sts377 are involved in the ADI pathway. The present study provided valuable information for the functional study of sRNAs in S. thermophilus and indicated a future research direction for sRNA in S. thermophilus. Overall, our results provided new insights for understanding the complex regulatory network of sRNAs in S. thermophilus.
Highlights
Small regulatory RNAs, generally 50–400 nt in length, are well established as key genetic regulators in prokaryotes (Wagner and Romby, 2015). sRNAs act as crucial regulators in various processes by exerting posttranscriptional control of gene expression by binding to target genes (Massé and Gottesman, 2002; Jacques et al, 2006)
Through small RNA sequencing, we searched for cDNA clusters that occurred within intergenic regions and discovered 135 clusters that represent possible intergenic sRNA candidates, including some previously identified sRNAs, such as 6S RNA and tmRNA
To cope with huge environmental fluctuations, microorganisms have evolved various mechanisms to maintain cell homeostasis. sRNA has been shown to play an important role under various stress conditions in other bacteria (Gottesman et al, 2006; Romby and Charpentier, 2010; Hoe et al, 2013), and it plays a vital role in regulating growth, adaptation and survival through posttranscriptional control of gene expression in bacterial cells (Wagner and Romby, 2015; van der Meulen et al, 2017)
Summary
Small regulatory RNAs (sRNAs), generally 50–400 nt in length, are well established as key genetic regulators in prokaryotes (Wagner and Romby, 2015). sRNAs act as crucial regulators in various processes by exerting posttranscriptional control of gene expression by binding to target genes (Massé and Gottesman, 2002; Jacques et al, 2006). In addition to enhancing or inhibiting mRNA degradation and/or translation by base pairing with mRNA targets, some sRNAs affect the activity of regulatory proteins by chelating regulatory proteins, thereby regulating gene expression (Klein and Raina, 2017). SRNA s015 directly combines with the target genes pG, busAB, cysD, ilvB, tcsR, ung, yudD, and ywdA in L. lactis F44 and improves the expression of these genes. In Lactobacillus casei-Pediococcus, sRNA rli plays an important role in inhibiting the synthesis of lactic acid, regulating the growth of cells in the logarithmic phase, and maintaining the survival of cells in the stationary phase (Wang et al, 2018; Yuki et al, 2020)
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