TraJ 5' UTR

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traJ 5' UTR

RF00243.jpg

Identifiers
Symbol traJ_5
Rfam RF00243
Other data
RNA type Cis-reg
Domain(s) Bacteria
SO 0000204

The traJ 5' UTR is a cis acting RNA element which is involved in regulating plasmid transfer in bacteria.

In conjugating bacteria the FinOP system regulates the transfer of F-like plasmids. The FinP gene encodes an antisense RNA product that is complementary to part of the 5' UTR of the traJ mRNA. [1] The traJ gene encodes a protein required for transcription from the major transfer promoter, pY. The FinO protein is essential for effective repression, acting by binding to FinP and protecting it from RNase E degradation.

Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus.

The fertility factor allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation. The F factor is carried on the F episome, the first episome to be discovered. Unlike other plasmids, F factor is constitutive for transfer proteins due to a mutation in the gene finO. The F plasmid belongs to a class of conjugative plasmids that control sexual functions of bacteria with a fertility inhibition (Fin) system.

FinP

FinP encodes an antisense non-coding RNA gene that is complementary to part of the TraJ 5' UTR. The FinOP system regulates the transfer of F-like plasmids. The traJ gene encodes a protein required for transcription from the major transfer promoter, pY. The FinO protein is essential for effective repression, acting by binding to FinP and protecting it from RNase E degradation.

Related Research Articles

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Bacillus-plasmid RNA motif

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Chlorobi-RRM RNA motif

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<i>lactis</i>-plasmid RNA motif

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PhotoRC RNA motifs

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RMF RNA motif

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Rne-II RNA motif

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TraJ-II RNA motif

The traJ-II RNA motif is a conserved RNA structure discovered in bacteria by using bioinformatics. traJ-II RNAs appear to be in the 5' untranslated regions of protein-coding genes called traJ, which functions in the process of bacterial conjugation. A previously identified motif known as TraJ 5' UTR is also found upstream of traJ genes functions as the target of FinP antisense RNAs, so it is possible that traJ-II RNAs play a similar role as targets of an antisense RNA. However, some sequence features within the traJ-II RNA motif suggest that the biological RNA might be transcribed from the reverse-complement strand. Thus is it unclear whether traJ-II function as cis-regulatory elements. traJ-II RNAs are found in a variety of proteobacteria.

YjdF RNA motif

The yjdF RNA motif is a conserved RNA structure identified using bioinformatics. Most yjdF RNAs are located in bacteria classified within the phylum Firmicutes. A yjdF RNA is found in the presumed 5' untranslated region of the yjdF gene in Bacillus subtilis, and almost all yjdF RNAs are found in the 5' UTRs of homologs of this gene. The function of the yjdF gene is unknown, but the protein that it is predicted to encode is classified by the Pfam Database as DUF2992.

PtaRNA1

PtaRNA1 is a family of non-coding RNAs. 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.

Toxin-antitoxin system

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Plasmid-mediated resistance

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par stability determinant

The par stability determinant is a 400 bp locus of the pAD1 plasmid which encodes a type I toxin-antitoxin system in Enterococcus faecalis. It was the first such plasmid addiction module to be found in gram-positive bacteria.

ZEB2-AS1 non-coding RNA in the species Homo sapiens

ZEB2-AS1 is a long non-coding RNA, which is overlapping and antisense to the ZEB2 gene. It overlaps the 5' splice site of an intron within the 5'UTR of the ZEB2 gene. This intron contains an internal ribosome entry site (IRES), which is necessary for ZEB2 expression. ZEB2-AS1 prevents the splicing of this intron, and therefore activates ZEB2 expression.

References

  1. Arthur DC, Ghetu AF, Gubbins MJ, Edwards RA, Frost LS, Glover JN (2003). "FinO is an RNA chaperone that facilitates sense-antisense RNA interactions". EMBO J. 22 (23): 6346–55. doi:10.1093/emboj/cdg607. PMC   291848 Lock-green.svg. PMID   14633993.