Summary: Toxin Ibs, type I toxin-antitoxin system
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Sib RNA Edit Wikipedia article
|Alt. Symbols||Sib RNA, QUAD RNA|
|RNA type||Gene; sRNA|
|Ibs Toxin of Type I toxin-antitoxin system|
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. 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.
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). 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. 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.
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. The constitutively expressed Sib transcript regulates the ibs (induction brings stasis) open reading frame which encodes a small 18â€“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 complementary, so the antisense-binding of Sib RNA with the ibs mRNA brings about dsRNA-mediated degradation.
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.
- Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12". Res. Microbiol. 150 (9â€“10): 653â€“664. doi:10.1016/S0923-2508(99)00126-6. PMID 10673004.
- 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): 1076â€“1093. doi:10.1111/j.1365-2958.2008.06394.x. PMC 2597788. PMID 18710431.
- 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): 1637â€“1651. doi:10.1101/gad.901001. PMC 312727. PMID 11445539.
- 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. 2012â€“2040. American Society for Microbiology, Washington, D.C.
- 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): 333â€“349. doi:10.1046/j.1365-2958.2002.03042.x. PMID 12123448.
- Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G (June 2010). "Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families". Nucleic Acids Res. 38 (11): 3743â€“3759. doi:10.1093/nar/gkq054. PMC 2887945. PMID 20156992. Retrieved 2010-08-11.
- Han K, Kim KS, Bak G, Park H, Lee Y (2010). "Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family". Nucleic Acids Res. 38 (17): 5851â€“5866. doi:10.1093/nar/gkq292. PMC 2943612. PMID 20453032.
- Hayashi K, Morooka N, Yamamoto Y, et al. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110". Mol. Syst. Biol. 2 (1): 2006.0007. doi:10.1038/msb4100049. PMC 1681481. PMID 16738553.
- Papenfort K, Vogel J (July 2010). "Regulatory RNA in bacterial pathogens". Cell Host Microbe. 8 (1): 116â€“127. doi:10.1016/j.chom.2010.06.008. PMID 20638647.
- Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12". Res. Microbiol. 150 (9â€“10): 653â€“664. doi:10.1016/S0923-2508(99)00126-6. PMID 10673004.
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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 .
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
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Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Number in seed:||4|
|Number in full:||14|
|Average length of the domain:||18.70 aa|
|Average identity of full alignment:||74 %|
|Average coverage of the sequence by the domain:||100.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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