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| Status |
Public on Feb 03, 2010 |
| Title |
Identification and function of non-coding small RNAs in Streptococcus pneumoniae |
| Organism |
Streptococcus pneumoniae |
| Experiment type |
Expression profiling by array
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| Summary |
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 ΔciaR 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 ΔciaR 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.
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| Overall design |
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.
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| Contributor(s) |
Tsui HT, Ray VA, Mukherjee D, Sham L, Wayne KJ, Feig AL, Winkler ME |
| Citation(s) |
19854910 |
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| Submission date |
Feb 03, 2009 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Ho-Ching Tiffany Tsui |
| E-mail(s) |
tttsui@indiana.edu
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| Phone |
(812)856-1781
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| Organization name |
Indiana University
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| Department |
Biology
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| Street address |
1001 E. Third St.
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47401 |
| Country |
USA |
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| Platforms (1) |
| GPL536 |
MWG Streptococcus pneumoniae Array |
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| Samples (3) |
| GSM365389 |
spnD39_ccnA_IU2841vsIU2678_BHI_rep1 |
| GSM365394 |
spnD39_ccnA_IU2841vsIU2678_BHI_rep2 |
| GSM365395 |
spnD39_ccnA_IU2841vsIU2678_BHI_rep3 |
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| Relations |
| BioProject |
PRJNA111677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE14688_RAW.tar |
1.1 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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