Journal article

Publication year: 2012

Journal: BMC Genomics

Volume number: 13

ISSN: 1471-2164

Open access status: Gold

DOI Link: https://doi.org/10.1186/1471-2164-13-550

Publisher: BioMed Central

Abstract: 

Background: Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49), employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases.

Results: We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 50 rapid amplification of cDNA ends-PCR (RACE-PCR) analysis.

Conclusions: In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of sRNAs expressed by a given organism requires the complementary use of different methods and the investigation of several environmental conditions. Despite a high conservation of sRNA genes within streptococci, the expression of sRNAs appears to be strain specific.

Harvard Citation style: Patenge, N., Billion, A., Raasch, P., Normann, J., Wisniewska-Kucper, A., Retey, J., et al. (2012) Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays, BMC Genomics, 13, Article 550. https://doi.org/10.1186/1471-2164-13-550

APA Citation style: Patenge, N., Billion, A., Raasch, P., Normann, J., Wisniewska-Kucper, A., Retey, J., Boisguerin, V., Hartsch, T., Hain, T., & Kreikemeyer, B. (2012). Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays. BMC Genomics. 13, Article 550. https://doi.org/10.1186/1471-2164-13-550