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SR1--a small RNA with two remarkably conserved functions.

Gimpel M, Preis H, Barth E, Gramzow L, Brantl S - Nucleic Acids Res. (2012)

Bottom Line: In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species.In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved.In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.

View Article: PubMed Central - PubMed

Affiliation: AG Bakteriengenetik, Lehrstuhl für Mikrobiologie und Mikrobengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany.

ABSTRACT
SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.

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Related in: MedlinePlus

BSs for CcpN in the promoter regions of sr1 homologues. The DNA sequences around the promoter regions of the sr1 homologues are shown. −35 and −10 boxes are in bold and underlined. Putative transcription start sites are shaded in light grey. The two putative BSs for CcpN are indicated in dark grey. The consensus sequence for the CcpN BS is TRTGHYATAYW (27), thereby R = purine, Y = pyrimidine, W = A or T, H = A, C or T.
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gks895-F2: BSs for CcpN in the promoter regions of sr1 homologues. The DNA sequences around the promoter regions of the sr1 homologues are shown. −35 and −10 boxes are in bold and underlined. Putative transcription start sites are shaded in light grey. The two putative BSs for CcpN are indicated in dark grey. The consensus sequence for the CcpN BS is TRTGHYATAYW (27), thereby R = purine, Y = pyrimidine, W = A or T, H = A, C or T.

Mentions: The B. subtilis sr1 gene is transcribed from a perfect consensus promoter with the −35 box TTGACA and the −10 box TAATAT separated by a 17 bp spacer. A comparison of the promoters of all sr1 homologues revealed that all of them have −35 and −10 boxes separated by a 17 bp spacer region (Figure 2). The only exception is Brev. brevis psr1, which has an 18 bp spacer. All −10 boxes in the B. cereus group display the sequence TAAAAT, whereas in all other cases, either TAATAT (as in B. subtilis) or TATTAT is found, and, again, in Brev. Brevis deviantly TAAGAT. All −35 boxes have the consensus sequence TTGACD with D being A, G or T. The putative transcription start site is always an A, expect in B. pumilus, where it is G.Figure 2.


SR1--a small RNA with two remarkably conserved functions.

Gimpel M, Preis H, Barth E, Gramzow L, Brantl S - Nucleic Acids Res. (2012)

BSs for CcpN in the promoter regions of sr1 homologues. The DNA sequences around the promoter regions of the sr1 homologues are shown. −35 and −10 boxes are in bold and underlined. Putative transcription start sites are shaded in light grey. The two putative BSs for CcpN are indicated in dark grey. The consensus sequence for the CcpN BS is TRTGHYATAYW (27), thereby R = purine, Y = pyrimidine, W = A or T, H = A, C or T.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526287&req=5

gks895-F2: BSs for CcpN in the promoter regions of sr1 homologues. The DNA sequences around the promoter regions of the sr1 homologues are shown. −35 and −10 boxes are in bold and underlined. Putative transcription start sites are shaded in light grey. The two putative BSs for CcpN are indicated in dark grey. The consensus sequence for the CcpN BS is TRTGHYATAYW (27), thereby R = purine, Y = pyrimidine, W = A or T, H = A, C or T.
Mentions: The B. subtilis sr1 gene is transcribed from a perfect consensus promoter with the −35 box TTGACA and the −10 box TAATAT separated by a 17 bp spacer. A comparison of the promoters of all sr1 homologues revealed that all of them have −35 and −10 boxes separated by a 17 bp spacer region (Figure 2). The only exception is Brev. brevis psr1, which has an 18 bp spacer. All −10 boxes in the B. cereus group display the sequence TAAAAT, whereas in all other cases, either TAATAT (as in B. subtilis) or TATTAT is found, and, again, in Brev. Brevis deviantly TAAGAT. All −35 boxes have the consensus sequence TTGACD with D being A, G or T. The putative transcription start site is always an A, expect in B. pumilus, where it is G.Figure 2.

Bottom Line: In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species.In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved.In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.

View Article: PubMed Central - PubMed

Affiliation: AG Bakteriengenetik, Lehrstuhl für Mikrobiologie und Mikrobengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany.

ABSTRACT
SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.

Show MeSH
Related in: MedlinePlus