Ivy-DE RNA motif: Difference between revisions
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{{Short description|Conserved DNA structure}} |
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{{primary sources|date=November 2021}} |
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{{DISPLAYTITLE:ivy-DE RNA motif}} |
{{DISPLAYTITLE:ivy-DE RNA motif}} |
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{{Infobox rfam |
{{Infobox rfam |
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The '''ivy-DE RNA motif''' is a conserved [[RNA]] structure that was [[Bioinformatics discovery of non-coding RNAs|discovered by bioinformatics]].<ref name="Weinberg2017b">{{cite journal |vauthors=Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR |title=Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions |journal=Nucleic Acids Res. |volume=45 |issue=18 |pages= |
The '''ivy-DE RNA motif''' is a conserved [[RNA]] structure that was [[Bioinformatics discovery of non-coding RNAs|discovered by bioinformatics]].<ref name="Weinberg2017b">{{cite journal |vauthors=Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR |title=Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions |journal=Nucleic Acids Res. |volume=45 |issue=18 |pages=10811–10823 |date=October 2017 |pmid=28977401 |pmc=5737381 |doi=10.1093/nar/gkx699 }}</ref> |
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ivy-DE motifs are found in the [[genus]] ''[[Pseudomonas]]''. |
ivy-DE motifs are found in the [[genus]] ''[[Pseudomonas]]''. |
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However, the RNA is most likely located in the [[three prime untranslated region|3′ UTR]] of the regulated (upstream) genes, even though ''cis''-regulatory RNAs in bacteria generally reside in the [[five prime untranslated region|5′ UTR]]. No genetic elements are consistently located downstream of ivy-DE motif RNAs, so the RNAs could be regulators within the 3′ UTR. However, it is possible that they are co-transcribed with the upstream genes and function rather as [[small RNA]]s. |
However, the RNA is most likely located in the [[three prime untranslated region|3′ UTR]] of the regulated (upstream) genes, even though ''cis''-regulatory RNAs in bacteria generally reside in the [[five prime untranslated region|5′ UTR]]. No genetic elements are consistently located downstream of ivy-DE motif RNAs, so the RNAs could be regulators within the 3′ UTR. However, it is possible that they are co-transcribed with the upstream genes and function rather as [[small RNA]]s. |
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ivy-DE motif RNAs are downstream of ivy (inhibitor of vertebrate lysozyme) genes. ivy [[protein]]s are used by bacteria and have shown to be potent inhibitors of vertebrate [[lysozyme]]s (see [http://pfam.xfam.org/family/Ivy]). However, other biological functions have been proposed.<ref name="Clarke2010">{{cite journal |vauthors=Clarke CA, Scheurwater EM, Clarke AJ |title=The vertebrate lysozyme inhibitor Ivy functions to inhibit the activity of lytic transglycosylase |journal=J. Biol. Chem. |volume=285 |issue=20 |pages=14843–14847 |date=May 2010 |pmid=20351104 |pmc=2865275 |doi=10.1074/jbc.C110.120931 | |
ivy-DE motif RNAs are downstream of ivy (inhibitor of vertebrate lysozyme) genes. ivy [[protein]]s are used by bacteria and have shown to be potent inhibitors of vertebrate [[lysozyme]]s (see [http://pfam.xfam.org/family/Ivy]). However, other biological functions have been proposed.<ref name="Clarke2010">{{cite journal |vauthors=Clarke CA, Scheurwater EM, Clarke AJ |title=The vertebrate lysozyme inhibitor Ivy functions to inhibit the activity of lytic transglycosylase |journal=J. Biol. Chem. |volume=285 |issue=20 |pages=14843–14847 |date=May 2010 |pmid=20351104 |pmc=2865275 |doi=10.1074/jbc.C110.120931 |doi-access=free }}</ref> Additionally, at least in ''Pseudomonas aeruginosa'' PAO1, the RNA is associated with a gene that encodes a homolog of the ivy protein that does not actually inhibit lysozyme.<ref name="Clarke2010"/> The function of this gene is unknown, but its expression increases in bacterial strains that overexpress the [[PhrS]] small RNA<ref>{{cite journal |vauthors=Sonnleitner E, Gonzalez N, Sorger-Domenigg T, Heeb S, Richter AS, Backofen R, Williams P, Hüttenhofer A, Haas D, Bläsi U |title=The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal |journal=Mol. Microbiol. |volume=80 |issue=4 |pages=868–885 |date=May 2011 |pmid=21375594 |doi=10.1111/j.1365-2958.2011.07620.x |doi-access= }}</ref> and during hypoxic growth.<ref>{{cite journal |vauthors=Alvarez-Ortega C, Harwood CS |title=Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration |journal=Mol. Microbiol. |volume=65 |issue=1 |pages=153–165 |date=July 2007 |pmid=17581126 |pmc=4157922 |doi=10.1111/j.1365-2958.2007.05772.x }}</ref> |
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==References== |
==References== |
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Latest revision as of 21:41, 6 October 2024
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| ivy-DE | |
|---|---|
 Consensus secondary structure and sequence conservation of ivy-DE RNA | |
| Identifiers | |
| Symbol | ivy-DE |
| Rfam | RF02999 |
| Other data | |
| RNA type | Cis-reg |
| SO | SO:0005836 |
| PDB structures | PDBe |
The ivy-DE RNA motif is a conserved RNA structure that was discovered by bioinformatics.[1] ivy-DE motifs are found in the genus Pseudomonas.
ivy-DE motif RNAs likely function as cis-regulatory elements, in view of their positions that are consistently downstream of protein-coding genes. However, the RNA is most likely located in the 3′ UTR of the regulated (upstream) genes, even though cis-regulatory RNAs in bacteria generally reside in the 5′ UTR. No genetic elements are consistently located downstream of ivy-DE motif RNAs, so the RNAs could be regulators within the 3′ UTR. However, it is possible that they are co-transcribed with the upstream genes and function rather as small RNAs.
ivy-DE motif RNAs are downstream of ivy (inhibitor of vertebrate lysozyme) genes. ivy proteins are used by bacteria and have shown to be potent inhibitors of vertebrate lysozymes (see [1]). However, other biological functions have been proposed.[2] Additionally, at least in Pseudomonas aeruginosa PAO1, the RNA is associated with a gene that encodes a homolog of the ivy protein that does not actually inhibit lysozyme.[2] The function of this gene is unknown, but its expression increases in bacterial strains that overexpress the PhrS small RNA[3] and during hypoxic growth.[4]
References
[edit]- ^ Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.
- ^ a b Clarke CA, Scheurwater EM, Clarke AJ (May 2010). "The vertebrate lysozyme inhibitor Ivy functions to inhibit the activity of lytic transglycosylase". J. Biol. Chem. 285 (20): 14843–14847. doi:10.1074/jbc.C110.120931. PMC 2865275. PMID 20351104.
- ^ Sonnleitner E, Gonzalez N, Sorger-Domenigg T, Heeb S, Richter AS, Backofen R, Williams P, Hüttenhofer A, Haas D, Bläsi U (May 2011). "The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal". Mol. Microbiol. 80 (4): 868–885. doi:10.1111/j.1365-2958.2011.07620.x. PMID 21375594.
- ^ Alvarez-Ortega C, Harwood CS (July 2007). "Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration". Mol. Microbiol. 65 (1): 153–165. doi:10.1111/j.1365-2958.2007.05772.x. PMC 4157922. PMID 17581126.