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Open Access Research article

Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays

Ranjit Kumar12, Pratik Shah67, Edwin Swiatlo5, Shane C Burgess1234, Mark L Lawrence12 and Bindu Nanduri12*

Author Affiliations

1 Department of Basic sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

2 Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA

3 Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762, USA

4 MSU Life Sciences and Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762, USA

5 Research Service (151), Veterans Affairs Medical Center, Jackson, MS 39216, USA

6 Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216 USA

7 Departments of Molecular Biology and Microbiology and Molecular Genetics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA

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BMC Genomics 2010, 11:350  doi:10.1186/1471-2164-11-350

Published: 3 June 2010

Abstract

Background

The identification of non-coding transcripts in human, mouse, and Escherichia coli has revealed their widespread occurrence and functional importance in both eukaryotic and prokaryotic life. In prokaryotes, studies have shown that non-coding transcripts participate in a broad range of cellular functions like gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Streptococcus pneumoniae (pneumococcus), an obligate human respiratory pathogen responsible for significant worldwide morbidity and mortality. Tiling microarrays enable genome wide mRNA profiling as well as identification of novel transcripts at a high-resolution.

Results

Here, we describe a high-resolution transcription map of the S. pneumoniae clinical isolate TIGR4 using genomic tiling arrays. Our results indicate that approximately 66% of the genome is expressed under our experimental conditions. We identified a total of 50 non-coding small RNAs (sRNAs) from the intergenic regions, of which 36 had no predicted function. Half of the identified sRNA sequences were found to be unique to S. pneumoniae genome. We identified eight overrepresented sequence motifs among sRNA sequences that correspond to sRNAs in different functional categories. Tiling arrays also identified approximately 202 operon structures in the genome.

Conclusions

In summary, the pneumococcal operon structures and novel sRNAs identified in this study enhance our understanding of the complexity and extent of the pneumococcal 'expressed' genome. Furthermore, the results of this study open up new avenues of research for understanding the complex RNA regulatory network governing S. pneumoniae physiology and virulence.