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0  structures 21  species 0  interactions 21  sequences 1  architecture

Family: ptaRNA1_toxin (PF12703)

Summary: Toxin of toxin-antitoxin type 1 system

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PtaRNA1 Edit Wikipedia article

PtaRNA1
PtaRNA1 SS.png
PtaRNA1 consensus secondary structure
Identifiers
Symbol PtaRNA1
Rfam RF01811
Other data
RNA type antisense
Domain(s) Gammaproteobacteria
SO {{{SO}}}
ptaRNA1_toxin
Identifiers
Symbol Toxin to PtaRNA1 antitoxin, of type 1 toxin-antitoxin system
Pfam PF12703

PtaRNA1 (plasmid transferred antisense RNA) is a family of non-coding RNAs.[1] Homologs of PtaRNA1 can be found in the proteobacteria families, Betaproteobacteria and Gammaproteobacteria. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene. In Xanthomonas campestris pv. vesicatoria, this gene is annotated as XCV2162 and is included in the plasmid toxin family of proteins.

Distribution and function

Both PtaRNA1 and the adjacent coding gene, which only appear only in combination, have an erratic phylogenetic distribution. The distribution of ptaRNA1 is not congruent with the phylogeny of the host species as it is with other sRNA families such as Yfr1 and Yfr2.[2] This indicates that ptaRNA1 has undergone frequent horizontal gene transfer.[1] These observations are in accordance with those made of Type I toxin-antitoxin systems.[3]

In type I toxin-antitoxin systems, the gene expression of a toxic protein is regulated by a small non-coding RNA. Type I toxin-antitoxin loci are frequently found in both prokaryotic chromosomes and plasmids.[4][5] The secondary structure of ptaRNA1 is very similar to the E. coli FinP antisense RNA.[1][6] FinP is an antisense regulator of the cis-acting RNA element Traj,[6] the structural similarities imply ptaRNA1 is likely to be part of a complex regulatory network.[1]

See also

References

  1. ^ a b c d Findeiss S, Schmidtke C, Stadler PF, Bonas U (March 2010). "A novel family of plasmid-transferred anti-sense ncRNAs". RNA Biol. 7 (2): 120–4. doi:10.4161/rna.7.2.11184. PMID 20220307. Retrieved 2010-07-13. 
  2. ^ Voss B, Gierga G, Axmann IM, Hess WR (2007). "A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria". BMC Genomics. 8: 375. doi:10.1186/1471-2164-8-375. PMC 2190773Freely accessible. PMID 17941988. 
  3. ^ Fozo EM, Hemm MR, Storz G (December 2008). "Small toxic proteins and the antisense RNAs that repress them". Microbiol. Mol. Biol. Rev. 72 (4): 579–89, Table of Contents. doi:10.1128/MMBR.00025-08. PMC 2593563Freely accessible. PMID 19052321. 
  4. ^ Gerdes K, Wagner EG (April 2007). "RNA antitoxins". Curr. Opin. Microbiol. 10 (2): 117–24. doi:10.1016/j.mib.2007.03.003. PMID 17376733. 
  5. ^ Weaver KE (April 2007). "Emerging plasmid-encoded antisense RNA regulated systems". Curr. Opin. Microbiol. 10 (2): 110–6. doi:10.1016/j.mib.2007.03.002. PMID 17376732. 
  6. ^ a b Arthur DC, Ghetu AF, Gubbins MJ, Edwards RA, Frost LS, Glover JN (December 2003). "FinO is an RNA chaperone that facilitates sense-antisense RNA interactions". EMBO J. 22 (23): 6346–55. doi:10.1093/emboj/cdg607. PMC 291848Freely accessible. PMID 14633993. 

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 of toxin-antitoxin type 1 system Provide feedback

This family is the toxin of a type 1 toxin-antitoxin system which is found in a relatively widespread range of bacterial species. The species distribution suggests frequent horizontal gene transfer. In a type 1 system, as characterised for the plasmid-encoded E coli hok/sok system, the toxin-encoding stable mRNA encodes a protein which rapidly leads to cell death unless the translation is suppressed by a short-lived small RNA. The plasmid-encoded module prevents the growth of plasmid-free offspring, thus ensuring the persistence of the plasmid in the population. Plasmid-free cells arising after cell-division will be killed because the stable mRNA toxin is present while the comparably unstable anti-toxin is rapidly degraded. Where the system is transcribed chromosomally, the mechanism is poorly understood [1].

Literature references

  1. Findeiss S, Schmidtke C, Stadler PF, Bonas U;, RNA Biol. 2010;7:120-124.: A novel family of plasmid-transferred anti-sense ncRNAs. PUBMED:20220307 EPMC:20220307


This tab holds annotation information from the InterPro database.

InterPro entry IPR024640

This family is the toxin of a type 1 toxin-antitoxin system which is found in a relatively widespread range of bacterial species. The species distribution suggests frequent horizontal gene transfer. In a type 1 system, as characterised for the plasmid-encoded E coli hok/sok system, the toxin-encoding stable mRNA encodes a protein which rapidly leads to cell death unless the translation is suppressed by a short-lived small RNA. The plasmid-encoded module prevents the growth of plasmid-free offspring, thus ensuring the persistence of the plasmid in the population. Plasmid-free cells arising after cell-division will be killed because the stable mRNA toxin is present while the comparably unstable anti-toxin is rapidly degraded. Where the system is transcribed chromosomally, the mechanism is poorly understood [PUBMED:20220307].

Domain organisation

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(185)
Meta
(0)
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(6)
RP35
(17)
RP55
(20)
RP75
(35)
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  Seed
(4)
Full
(21)
Representative proteomes UniProt
(96)
NCBI
(185)
Meta
(0)
RP15
(6)
RP35
(17)
RP55
(20)
RP75
(35)
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Curation and family details

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Curation View help on the curation process

Seed source: Gardner P [1])
Previous IDs: plasmid_Toxin; PtaRNA1-toxin;
Type: Family
Sequence Ontology: SO:0100021
Author: Gardner P , Coggill P
Number in seed: 4
Number in full: 21
Average length of the domain: 72.00 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 71.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.4 19.0
Trusted cut-off 20.6 19.1
Noise cut-off 18.7 16.9
Model length: 73
Family (HMM) version: 7
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