Unknown,Transcriptomics,Genomics,Proteomics

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Identification and function of non-coding small RNAs in Streptococcus pneumoniae

ABSTRACT: We report here an experimental search for small non-coding RNAs in a low GC, gram-positive, human pathogenic bacteria Streptococcus pneumoniae. Based on the bioinformatic analyses by Livny et al. (2006, Nucleic Acids Res. 34:3484-93), we tested 36 candidates by Northern analyses and confirmed the expression of 8 novel and one previously-reported sRNAs (CcnA) in the genome of D39 serotype 2 strain. Some of the sRNAs showed differential expression in stationary phase or after treatment with competence stimulatory peptide compared to untreated exponential cells. One sRNA we detected is CcnA, one of five CiaR-controlled non-coding RNA (CcnA to E) reported previously. By ectopically expressing this sRNA in a ÎciaR strain, we provide evidence that CcnA plays important roles in the regulation of growth and chain length of S. pneumoniae. Microarray analysis comparing global gene expression of CcnA-expressing and CcnA-nonexpressing ÎciaR strains showed significant differences in expression of competence related genes and five putative transcriptional regulators. QPCR and transformation assays further confirmed that CcnA sRNA mediates a strong negative effect on competence development. Our findings suggested many of the CiaRH function may be mediated via Ccn sRNAs and that sRNAs play regulatory roles in S. pneumoniae, an organism that lacks Hfq RNA chaperone. Three independent hybridizations using independent RNA preparations from the strain IU2678 (a ciaR knockout strain with no ccnA expression, reference strain) and strain IU2841 (a ciaR knowckout strain with ccnA expression at an ectopic site) were performed. Dye swap was performed with the reference strain labeled with Cy3 in two hybridizations and Cy5 in the one hybridizations.

ORGANISM(S): Streptococcus pneumoniae

SUBMITTER: Kyle Wayne

PROVIDER: E-GEOD-14688 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39.

Tsui Ho-Ching Tiffany HC Mukherjee Dhriti D Ray Valerie A VA Sham Lok-To LT Feig Andrew L AL Winkler Malcolm E ME

Journal of bacteriology 20100101 1

We report a search for small RNAs (sRNAs) in the low-GC, gram-positive human pathogen Streptococcus pneumoniae. Based on bioinformatic analyses by Livny et al. (J. Livny, A. Brencic, S. Lory, and M. K. Waldor, Nucleic Acids Res. 34:3484-3493, 2006), we tested 40 candidates by Northern blotting and confirmed the expression of nine new and one previously reported (CcnA) sRNAs in strain D39. CcnA is one of five redundant sRNAs reported by Halfmann et al. (A. Halfmann, M. Kovacs, R. Hakenbeck, and R ...[more]

PMID: 19854910

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Dataset Information

Identification and function of non-coding small RNAs in Streptococcus pneumoniae

Publications

Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39.

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