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Novel regulatory small RNAs in Streptococcus pyogenes.

Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH - PLoS ONE (2013)

Bottom Line: Through this process, we discovered 7 putative novel trans-acting sRNAs.Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals.Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Southern Illinois University, Carbondale, Illinois, United States of America.

ABSTRACT
Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in computational prediction, we employed a combination of three different computational algorithms (sRNAPredict, eQRNA and RNAz). A total of 45 candidates were chosen based on the computational analysis, and their transcription was analyzed by reverse-transcriptase PCR and Northern blot. Through this process, we discovered 7 putative novel trans-acting sRNAs. Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals. Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis. This study provides a significant resource for future study of small RNAs and their roles in physiology and pathogenesis of S. pyogenes.

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Related in: MedlinePlus

The abundance of newly discovered streptococcal small RNA candidates (SSRCs) varied between growth phases.A) The intracellular abundance of SSRCs at different growth phases. The abundance of each SSRC was determined over the course of growth (exponential phase, EX; early stationary phase, ES; late stationary phase, LS) through Northern blotting. Size markers (S) were run and their sizes are indicated at the left sides of Northern blots. The abundance of 5S RNA (5S) was also determined as a loading control and shown below each Northern blot. B) Abundance of each intracellular sRNA relative to that at the exponential growth phase. Abundance of sRNAs on Northern blots was determined by densitometry, normalized with the abundance of 5S RNA, and expressed relative to the abundance at the exponential growth phase.
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pone-0064021-g004: The abundance of newly discovered streptococcal small RNA candidates (SSRCs) varied between growth phases.A) The intracellular abundance of SSRCs at different growth phases. The abundance of each SSRC was determined over the course of growth (exponential phase, EX; early stationary phase, ES; late stationary phase, LS) through Northern blotting. Size markers (S) were run and their sizes are indicated at the left sides of Northern blots. The abundance of 5S RNA (5S) was also determined as a loading control and shown below each Northern blot. B) Abundance of each intracellular sRNA relative to that at the exponential growth phase. Abundance of sRNAs on Northern blots was determined by densitometry, normalized with the abundance of 5S RNA, and expressed relative to the abundance at the exponential growth phase.

Mentions: We determined the intracellular abundance of the putative trans-acting SSRCs at the exponential (EX), early stationary (ES), and late stationary (LS) growth phases of cells through Northern blotting (Figure 4). Agreeing with a previously reported result, FasX was most abundant at the exponential phase [20]. Most SSRCs exhibited variation of abundance between growth phases and were expressed abundantly at the exponential and early stationary phase and least abundantly at the late stationary phase. The abundance of SSRC 8, 10, 21, 29, 30, and 38 was dramatically reduced at the late stationary phase, showing a similar pattern to that of the FasX transcript over the course of growth. On the other hand, SSRC 34 and 41 exhibited similar abundance throughout all growth phases.


Novel regulatory small RNAs in Streptococcus pyogenes.

Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH - PLoS ONE (2013)

The abundance of newly discovered streptococcal small RNA candidates (SSRCs) varied between growth phases.A) The intracellular abundance of SSRCs at different growth phases. The abundance of each SSRC was determined over the course of growth (exponential phase, EX; early stationary phase, ES; late stationary phase, LS) through Northern blotting. Size markers (S) were run and their sizes are indicated at the left sides of Northern blots. The abundance of 5S RNA (5S) was also determined as a loading control and shown below each Northern blot. B) Abundance of each intracellular sRNA relative to that at the exponential growth phase. Abundance of sRNAs on Northern blots was determined by densitometry, normalized with the abundance of 5S RNA, and expressed relative to the abundance at the exponential growth phase.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3675131&req=5

pone-0064021-g004: The abundance of newly discovered streptococcal small RNA candidates (SSRCs) varied between growth phases.A) The intracellular abundance of SSRCs at different growth phases. The abundance of each SSRC was determined over the course of growth (exponential phase, EX; early stationary phase, ES; late stationary phase, LS) through Northern blotting. Size markers (S) were run and their sizes are indicated at the left sides of Northern blots. The abundance of 5S RNA (5S) was also determined as a loading control and shown below each Northern blot. B) Abundance of each intracellular sRNA relative to that at the exponential growth phase. Abundance of sRNAs on Northern blots was determined by densitometry, normalized with the abundance of 5S RNA, and expressed relative to the abundance at the exponential growth phase.
Mentions: We determined the intracellular abundance of the putative trans-acting SSRCs at the exponential (EX), early stationary (ES), and late stationary (LS) growth phases of cells through Northern blotting (Figure 4). Agreeing with a previously reported result, FasX was most abundant at the exponential phase [20]. Most SSRCs exhibited variation of abundance between growth phases and were expressed abundantly at the exponential and early stationary phase and least abundantly at the late stationary phase. The abundance of SSRC 8, 10, 21, 29, 30, and 38 was dramatically reduced at the late stationary phase, showing a similar pattern to that of the FasX transcript over the course of growth. On the other hand, SSRC 34 and 41 exhibited similar abundance throughout all growth phases.

Bottom Line: Through this process, we discovered 7 putative novel trans-acting sRNAs.Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals.Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Southern Illinois University, Carbondale, Illinois, United States of America.

ABSTRACT
Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in computational prediction, we employed a combination of three different computational algorithms (sRNAPredict, eQRNA and RNAz). A total of 45 candidates were chosen based on the computational analysis, and their transcription was analyzed by reverse-transcriptase PCR and Northern blot. Through this process, we discovered 7 putative novel trans-acting sRNAs. Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals. Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis. This study provides a significant resource for future study of small RNAs and their roles in physiology and pathogenesis of S. pyogenes.

Show MeSH
Related in: MedlinePlus