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0  structures 15  species 0  interactions 33  sequences 1  architecture

Family: Ibs_toxin (PF13956)

Summary: Toxin Ibs, type I toxin-antitoxin system

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This is the Wikipedia entry entitled "Sib RNA". More...

Sib RNA Edit Wikipedia article

Sib RNA
RF00113.jpg
Predicted secondary structure and sequence conservation of QUAD
Identifiers
Symbol QUAD
Alt. Symbols Sib RNA, QUAD RNA
Rfam RF00113
Other data
RNA type Gene; sRNA
Domain(s) Bacteria
SO 0000655
Ibs Toxin of Type I toxin-antitoxin system
Identifiers
Symbol Ibs_toxin
Pfam PF13957

Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions.[1] The family was later renamed Sib (for short intergenic abundant sequences) when it was discovered that the number of repeats is variable in other species and in other E. coli strains.[2]

Contents

[edit] Identification

These small RNA were identified computationally by searching the genome of E. coli for intergenic regions of high sequence identity (sequence conservation) with the genomes of closely related bacteria (several salmonella species and Klebsiella pneumoniae).[3] This data was combined with microarray expression analysis and potential novel ncRNAs identified. The expression of novel ncRNA of interest was confirmed by northern blotting.

In this large scale screen these ncRNAs were simply referred to as candidates 43, 55 and 61.[3] These 3 ncRNA appear to be highly homologous and are derived from a repeat region of the genome. Each of the ncRNA contains a short stretch homologous to boxC, a repeat element of unknown function present in 50 copies or more within the genome of E. coli.[4]

[edit] Function

Sib RNA regulates the expression of a toxic protein in a type I toxin-antitoxin system similar to that of hok/sok andldr-rdl genes.[5] The constitutively expressed Sib transcript regulates the ibs (induction brings stasis) open reading frame which encodes a small 18-19 amino acid hydrophobic protein which slows growth at moderate levels of expression and is toxic when overexpressed. The ibs gene is on the opposite strand to sib and is completely complimentary, so the antisense-binding of Sib RNA with the ibs mRNA brings about dsRNA-mediated degradation.[2]

When sib was deleted in multi-copy plasmids, the cells could not be maintained due to the toxicity of the unrepressed ibs protein. The toxicity mechanism of ibs protein is not fully understood, but a change in membrane potential upon over-expression of the protein suggests that interactions with membrane proteins or membrane insertion brings about cell death.[2]

[edit] See also

[edit] References

  1. ^ Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12". Res. Microbiol. 150 (9-10): 653–64. doi:10.1016/S0923-2508(99)00126-6. PMID 10673004. 
  2. ^ a b c Fozo EM, Kawano M, Fontaine F, et al. (December 2008). "Repression of small toxic protein synthesis by the Sib and OhsC small RNAs". Mol. Microbiol. 70 (5): 1076–93. doi:10.1111/j.1365-2958.2008.06394.x. PMC 2597788. PMID 18710431. Retrieved 2010-08-11. 
  3. ^ a b Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays". Genes Dev. 15 (13): 1637–51. doi:10.1101/gad.901001. PMC 312727. PMID 11445539. 
  4. ^ Bachellier, S., Gilson, E., Hofnung, M., and Hill, C.W. 1996. Repeated sequences. In Escherichia coli and Salmonella: Cellular and molecular biology (ed. F.C. Neidhardt, et al.), pp. 2012-2040. American Society for Microbiology, Washington, D.C.
  5. ^ Kawano M, Oshima T, Kasai H, Mori H (July 2002). "Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli". Mol. Microbiol. 45 (2): 333–49. doi:10.1046/j.1365-2958.2002.03042.x. PMID 12123448. Retrieved 2010-08-11. 

[edit] Further reading

[edit] External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Toxin Ibs, type I toxin-antitoxin system Provide feedback

The Ibs (induction brings stasis) proteins are a family of toxic peptides. Their expression is inhibited by the Sib antisense RNAs, which act as antitoxins [1].

Literature references

  1. Fozo EM, Kawano M, Fontaine F, Kaya Y, Mendieta KS, Jones KL, Ocampo A, Rudd KE, Storz G;, Mol Microbiol. 2008;70:1076-1093.: Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. PUBMED:18710431 EPMC:18710431


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025881

The Ibs (induction brings stasis) proteins are a family of toxic peptides. Their expression is inhibited by the Sib antisense RNAs, which act as antitoxins [PUBMED:18710431].

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Representative proteomes NCBI
(21)
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RP35
(5)
RP55
(5)
RP75
(5)
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Seed source: Jackhmmer:C1P607
Previous IDs: none
Type: Family
Author: Eberhardt R
Number in seed: 4
Number in full: 33
Average length of the domain: 18.80 aa
Average identity of full alignment: 77 %
Average coverage of the sequence by the domain: 64.41 %

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build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 33.3 33.0
Noise cut-off 22.5 22.4
Model length: 19
Family (HMM) version: 1
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