Asd RNA motif: Difference between revisions
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The ''' ''asd'' RNA motif''' is a conserved [[RNA]] structure found is certain [[lactic acid bacteria]]. The ''asd'' motif was detected by [[bioinformatics]]<ref name="Weinberg2010">{{cite journal |vauthors=Weinberg Z, Wang JX, Bogue J |title=Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes |journal=Genome Biol |volume=11 |issue=3 |pages=R31 |date=March 2010 |pmid=20230605 |doi=10.1186/gb-2010-11-3-r31 |url= |pmc=2864571|display-authors=etal}}</ref> and an individual ''asd'' RNA in ''[[Streptococcus pyogenes]]'' was detected by [[microarray]] and [[northern hybridization]] experiments as a 170-nucleotide molecule called "SR914400".<ref>{{cite journal |vauthors=Perez N, Treviño J, Liu Z, Ho SC, Babitzke P, Sumby P |title=A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus |journal=PLoS ONE |volume=4 |issue=11 |pages=e7668 |year=2009 |pmid=19888332 |pmc=2765633 |doi=10.1371/journal.pone.0007668 |url=}}</ref> The [[transcription start site]] determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram. |
The ''' ''asd'' RNA motif''' is a conserved [[RNA]] structure found is certain [[lactic acid bacteria]]. The ''asd'' motif was detected by [[bioinformatics]]<ref name="Weinberg2010">{{cite journal |vauthors=Weinberg Z, Wang JX, Bogue J |title=Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes |journal=Genome Biol |volume=11 |issue=3 |pages=R31 |date=March 2010 |pmid=20230605 |doi=10.1186/gb-2010-11-3-r31 |url= |pmc=2864571|display-authors=etal}}</ref> and an individual ''asd'' RNA in ''[[Streptococcus pyogenes]]'' was detected by [[microarray]] and [[northern hybridization]] experiments as a 170-nucleotide molecule called "SR914400".<ref>{{cite journal |vauthors=Perez N, Treviño J, Liu Z, Ho SC, Babitzke P, Sumby P |title=A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus |journal=PLoS ONE |volume=4 |issue=11 |pages=e7668 |year=2009 |pmid=19888332 |pmc=2765633 |doi=10.1371/journal.pone.0007668 |url=}}</ref> The [[transcription start site]] determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram. |
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Some ''asd'' RNAs are associated with genes, such as ''asd'', that are suggestive of a [[cis-regulatory element|cis-regulatory function]]. However, several lines of evidence suggest that this is not the biological role of ''asd'' RNAs. First, in some cases, the ''asd'' RNA is not in the [[5' untranslated region]] of any annotated [[gene]]. Second, in ''[[Streptococcus mutans]]'', there is a strong promoter<ref name="Cardineau1987">{{cite journal |vauthors=Cardineau GA, Curtiss R |title=Nucleotide sequence of the asd gene of Streptococcus mutans. Identification of the promoter region and evidence for attenuator-like sequences preceding the structural gene |journal=J. Biol. Chem. |volume=262 |issue=7 |pages=3344–53 |date=March 1987 |pmid=2434499 |doi= |url=}}</ref> immediately downstream of the transcription terminator that follows the ''asd'' RNA, and this promoter precedes the downstream gene. This arrangement suggests that ''asd'' RNA transcription is terminated, and the gene is transcribed from the downstream promoter. Finally, although the ''asd'' gene encodes an enzyme, [[aspartate-semialdehyde dehydrogenase]], that participates in the synthesis of [[methionine]], [[lysine]] and [[threonine]], transcription levels of the ''asd'' gene remain constant even when the concentrations of these amino acids are varied.<ref name="Cardineau1987"/> |
Some ''asd'' RNAs are associated with genes, such as ''asd'', that are suggestive of a [[cis-regulatory element|cis-regulatory function]].<ref>{{cite journal|title=Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalact|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448216/|first1=Elisabeth|last1=Sauvage|display-authors=etal|journal=BMC Genomics|date= 2015|volume=16|issue= 1 |page=419|doi=10.1186/s12864-015-1583-4}}</ref> However, several lines of evidence suggest that this is not the biological role of ''asd'' RNAs. First, in some cases, the ''asd'' RNA is not in the [[5' untranslated region]] of any annotated [[gene]]. Second, in ''[[Streptococcus mutans]]'', there is a strong promoter<ref name="Cardineau1987">{{cite journal |vauthors=Cardineau GA, Curtiss R |title=Nucleotide sequence of the asd gene of Streptococcus mutans. Identification of the promoter region and evidence for attenuator-like sequences preceding the structural gene |journal=J. Biol. Chem. |volume=262 |issue=7 |pages=3344–53 |date=March 1987 |pmid=2434499 |doi= |url=}}</ref> immediately downstream of the transcription terminator that follows the ''asd'' RNA, and this promoter precedes the downstream gene. This arrangement suggests that ''asd'' RNA transcription is terminated, and the gene is transcribed from the downstream promoter. Finally, although the ''asd'' gene encodes an enzyme, [[aspartate-semialdehyde dehydrogenase]], that participates in the synthesis of [[methionine]], [[lysine]] and [[threonine]], transcription levels of the ''asd'' gene remain constant even when the concentrations of these amino acids are varied.<ref name="Cardineau1987"/> |
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==References== |
==References== |
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Revision as of 01:13, 8 January 2018
| asd RNA motif | |
|---|---|
 Consensus secondary structure of asd RNAs. The stem marked "terminator" is predicted as a Rho-independent transcription terminator. | |
| Identifiers | |
| Symbol | asd RNA |
| Rfam | RF01732 |
| Other data | |
| RNA type | sRNA |
| Domain(s) | Streptococcaceae |
| SO | 0000655 |
| PDB structures | PDBe |
The asd RNA motif is a conserved RNA structure found is certain lactic acid bacteria. The asd motif was detected by bioinformatics[1] and an individual asd RNA in Streptococcus pyogenes was detected by microarray and northern hybridization experiments as a 170-nucleotide molecule called "SR914400".[2] The transcription start site determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram.
Some asd RNAs are associated with genes, such as asd, that are suggestive of a cis-regulatory function.[3] However, several lines of evidence suggest that this is not the biological role of asd RNAs. First, in some cases, the asd RNA is not in the 5' untranslated region of any annotated gene. Second, in Streptococcus mutans, there is a strong promoter[4] immediately downstream of the transcription terminator that follows the asd RNA, and this promoter precedes the downstream gene. This arrangement suggests that asd RNA transcription is terminated, and the gene is transcribed from the downstream promoter. Finally, although the asd gene encodes an enzyme, aspartate-semialdehyde dehydrogenase, that participates in the synthesis of methionine, lysine and threonine, transcription levels of the asd gene remain constant even when the concentrations of these amino acids are varied.[4]
References
- ^ Weinberg Z, Wang JX, Bogue J, et al. (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Perez N, Treviño J, Liu Z, Ho SC, Babitzke P, Sumby P (2009). "A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus". PLoS ONE. 4 (11): e7668. doi:10.1371/journal.pone.0007668. PMC 2765633. PMID 19888332.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Sauvage, Elisabeth; et al. (2015). "Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalact". BMC Genomics. 16 (1): 419. doi:10.1186/s12864-015-1583-4.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ a b Cardineau GA, Curtiss R (March 1987). "Nucleotide sequence of the asd gene of Streptococcus mutans. Identification of the promoter region and evidence for attenuator-like sequences preceding the structural gene". J. Biol. Chem. 262 (7): 3344–53. PMID 2434499.
External links
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