DsrA RNA
{{Short description|Non-coding RNA}}
{{Infobox rfam
| Name = DsrA RNA
| image = RF00014.jpg
| width =
| caption = Predicted secondary structure and sequence conservation of DsrA
| Symbol = DsrA
| AltSymbols =
| Rfam = RF00014
| miRBase =
| miRBase_family =
| Tax_domain = Bacteria
| GO =
| SO = {{SO|0000378}}
| CAS_number =
| EntrezGene =
| HGNCid =
| OMIM =
| PDB =
| RefSeq =
| Chromosome =
| Arm =
| Band =
| LocusSupplementaryData =
}}
DsrA RNA is a non-coding RNA that regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein,{{cite journal | last = Sledjeski | first = D |author2=Gottesman S | year = 1995 | title = A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli | journal = Proc Natl Acad Sci USA | volume = 92 | pages = 2003–2007 | pmid = 7534408 | doi = 10.1073/pnas.92.6.2003 | issue = 6 | pmc = 42411|bibcode = 1995PNAS...92.2003S | doi-access = free }} and translation, by promoting efficient translation of the stress sigma factor, RpoS.{{cite journal | last = Majdalani | first = N |author2=Cunning C |author3=Sledjeski D |author4=Elliott T |author5=Gottesman S | year = 1998 | title = DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription | journal = Proc Natl Acad Sci USA | volume = 95 | pages = 12462–12467 | pmid = 9770508 | doi = 10.1073/pnas.95.21.12462 | issue = 21 | pmc = 22853 | bibcode=1998PNAS...9512462M| doi-access = free }}{{cite journal | last = Gottesman | first = S | year = 2005 | title = Micros for microbes: non-coding regulatory RNAs in bacteria | journal = Trends Genet | volume = 21 | pages = 399–404 | pmid = 15913835 | doi = 10.1016/j.tig.2005.05.008 | issue = 7| citeseerx = 10.1.1.391.8944 }} These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. The structures of DsrA and DsrA/rpoS complex were studied by NMR. The study concluded that the sRNA contains a dynamic conformational equilibrium for its second stem–loop which might be an important mechanism for DsrA to regulate the translations of its multiple target mRNAs.{{Cite journal|last1=Wu|first1=Pengzhi|last2=Liu|first2=Xiaodan|last3=Yang|first3=Lingna|last4=Sun|first4=Yitong|last5=Gong|first5=Qingguo|last6=Wu|first6=Jihui|last7=Shi|first7=Yunyu|date=2017-09-19|title=The important conformational plasticity of DsrA sRNA for adapting multiple target regulation|journal=Nucleic Acids Research|volume=45|issue=16|pages=9625–9639|doi=10.1093/nar/gkx570|issn=1362-4962|pmid=28934467|pmc=5766208}}
There is evidence that DsrA RNA can self-assemble into nanostructures through antisense interactions of three self-complementary regions.{{cite journal |vauthors=Cayrol B, Nogues C, Dawid A, Sagi I, Silberzan P, Isambert H |title=A Nanostructure Made of a Bacterial Noncoding RNA. |journal=J Am Chem Soc |volume= 131|issue= 47|pages= 17270–17276|year=2009 |pmid=19821568 |doi=10.1021/ja906076e}}{{cite journal |doi= 10.4161/rna.6.4.8949 |vauthors=Cayrol B, Geinguenaud F, Lacoste J, Busi F, Le Dérout J, Piétrement O, Le Cam E, Régnier P, Lavelle C, Arluison V |title=Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences.. |journal= RNA Biol. |volume=6 |year=2009 |pmid=19535898 |issue= 4 |pages= 434–445|doi-access=free }}
Targets of DsrA
There is experimental evidence to suggest that DsrA interacts with the protein-coding genes hns,{{cite journal |doi=10.1073/pnas.95.21.12456 |vauthors=Lease RA, Cusick ME, Belfort M |title=Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. |journal=Proc Natl Acad Sci U S A |volume=95 |issue=21 |pages=12456–12461 |year=1998 |pmid=9770507 |pmc=22852 |bibcode=1998PNAS...9512456L|doi-access=free }}{{cite journal |doi=10.1093/nar/gkl1040 |vauthors=Urban JH, Vogel J |title=Translational control and target recognition by Escherichia coli small RNAs in vivo. |journal=Nucleic Acids Res |volume=35 |issue=3 |pages=1018–1037 |year=2007 |pmid=17264113 |pmc=1807950}}{{cite journal |doi=10.1073/pnas.170281497 |author=Lease RA Belfort M |title=A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. |journal=Proc Natl Acad Sci U S A |volume=97 |issue=18 |pages=9919–9924 |year=2000 |pmid=10954740 |pmc=27626 |bibcode=2000PNAS...97.9919L|doi-access=free }} rbsD, argR, ilvI and rpoS{{cite journal |doi=10.1073/pnas.95.21.12462 |vauthors=Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S |title=DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. |journal=Proc Natl Acad Sci U S A |volume=95 |issue=21 |pages=12462–12467 |year=1998 |pmid=9770508 |pmc=22853 |bibcode=1998PNAS...9512462M|doi-access=free }}{{cite journal |doi=10.1111/j.1365-2958.2001.02329.x |vauthors=Majdalani N, Chen S, Murrow J, St John K, Gottesman S |title=Regulation of RpoS by a novel small RNA: the characterization of RprA. |journal=Mol Microbiol |volume=39 |issue=5 |pages=1382–1394 |year=2001 |pmid=11251852|doi-access=free }}{{cite journal |vauthors=Sledjeski DD, Gupta A, Gottesman S |title=The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. |journal=EMBO J |volume=15 |issue=15 |pages=3993–4000 |year=1996 |pmid=8670904 |pmc=452119|doi=10.1002/j.1460-2075.1996.tb00773.x }}{{cite journal |doi=10.1128/JB.183.6.1997-2005.2001 |vauthors=Sledjeski DD, Whitman C, Zhang A |title=Hfq is necessary for regulation by the untranslated RNA DsrA. |journal=J Bacteriol |volume=183 |issue=6 |pages=1997–2005 |year=2001 |pmid=11222598 |pmc=95095}} via an anti-sense mechanism.
DsrA folds into a structure with three hairpins. The second of these (nucleotides 23–60) binds to Hfq.{{cite journal|last=Brescia|first=CC|author2=Mikulecky, PJ |author3=Feig, AL |author4= Sledjeski, DD |title=Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure.|journal=RNA|date=Jan 2003|volume=9|issue=1|pages=33–43|pmid=12554874|doi=10.1261/rna.2570803|pmc=1370368}}
References
{{reflist}}
Further reading
- {{Cite journal
| doi = 10.1128/AEM.03004-09
| pmc = 2916486
| title = Improved dsrA-based Terminal Restriction Fragment Length Polymorphism Analysis of Sulfate-Reducing Bacteria
| pmid = 20543035
| year = 2010
| pages = 5308–5311
| last1 = Santillano
| issue = 15 | first1 = D.
| last2 = Boetius
| volume = 76 | first2 = A.
| last3 = Ramette | first3 = A.
| journal = Applied and Environmental Microbiology
}}
- {{Cite journal
| doi = 10.1093/nar/gkp1125
| pmc = 2831331
| title = Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding
| pmid = 19969548
| year = 2009
| last1 = Vecerek | first1 = B.
| last2 = Beich-Frandsen | first2 = M.
| last3 = Resch | first3 = A.
| last4 = Blasi | first4 = U.
| journal = Nucleic Acids Research
| volume = 38
| issue = 4
| pages = 1284–1293
}}
- {{Cite journal
| doi = 10.1128/IAI.00819-08
| title = Localization of the Domains of the Haemophilus ducreyi Trimeric Autotransporter DsrA Involved in Serum Resistance and Binding to the Extracellular Matrix Proteins Fibronectin and Vitronectin
| year = 2008
| last1 = Leduc | first1 = I.
| last2 = Olsen | first2 = B.
| last3 = Elkins | first3 = C.
| journal = Infection and Immunity
| volume = 77
| pages = 657–666
| pmid = 19015257
| issue = 2
| pmc = 2632028
}}
- {{Cite journal| first1 = J. | first2 = A.
| title = The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
| last2 = Woodson
| url = http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=18658123
| format = Free full text
| journal = RNA
| last1 = Soper
| volume = 14
| issue = 9
| pages = 1907–1917
| date=Sep 2008 | issn = 1355-8382
| pmid = 18658123
| pmc = 2525945
| doi = 10.1261/rna.1110608
}}
- {{Cite journal
| doi = 10.1111/j.1574-6968.2008.01240.x
| pmid = 18616595
| title = RpoS, H-NS, and DsrA influence EHEC hemolysin operon (ehxCABD) transcription inEscherichia coliO157:H7 strain EDL933
| year = 2008
| last1 = Li | first1 = H.
| last2 = Granat | first2 = A.
| last3 = Stewart | first3 = V.
| last4 = Gillespie | first4 = J. R.
| journal = FEMS Microbiology Letters
| volume = 285
| issue = 2
| pages = 257–262
| doi-access = free
}}
- {{Cite journal
| doi = 10.1128/IAI.00994-07
| pmc = 2292853
| title = Outer Membrane Protein DsrA Is the Major Fibronectin-Binding Determinant of Haemophilus ducreyi
| pmid = 18212073
| year = 2008
| last1 = Leduc | first1 = I.
| last2 = White | first2 = C. D.
| last3 = Nepluev | first3 = I.
| last4 = Throm | first4 = R. E.
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| last6 = Elkins | first6 = C.
| journal = Infection and Immunity
| volume = 76
| issue = 4
| pages = 1608–1616
}}
- {{Cite journal
| doi = 10.1261/rna.603108
| pmc = 2248258
| title = Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5′-leader
| pmid = 18192613
| year = 2008
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| journal = RNA
| volume = 14
| issue = 3
| pages = 454–459
}}
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| doi = 10.1007/s00248-007-9233-2
| pmid = 17351812
| title = Quantification of Sulfate-reducing Bacteria in Industrial Wastewater, by Real-time Polymerase Chain Reaction (PCR) Using dsrA and apsA Genes
| year = 2007
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| journal = Microbial Ecology
| volume = 54
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| s2cid = 20554316
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| doi = 10.1016/j.bbrc.2006.07.102
| title = Interactions of ribosomal protein S1 with DsrA and rpoS mRNA☆
| pmid = 16890206
| year = 2006
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| doi = 10.1128/JB.00206-06
| pmc = 1539969
| title = Limited Role for the DsrA and RprA Regulatory RNAs in rpoS Regulation in Salmonella enterica
| pmid = 16816180
| year = 2006
| last1 = Jones | first1 = A. M.
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| journal = Journal of Bacteriology
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| doi = 10.1021/bi0523613
| pmid = 16605255
| title = Escherichia coliHfq Binds A18and DsrA Domain II with Similar 2:1 Hfq6/RNA Stoichiometry Using Different Surface Sites†
| year = 2006
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| journal = Biochemistry
| volume = 45
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| doi = 10.1093/jb/mvj045
| title = Evaluation of the Dynamic Structure of DsrA RNA from E. Coli and Its Functional Consequences
| pmid = 16567408
| year = 2006
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| journal = Journal of Biochemistry
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| doi = 10.1128/IAI.73.6.3431-3439.2005
| pmc = 1111860
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| pmid = 15908371
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- {{Cite journal
| doi = 10.1128/IAI.73.4.2387-2399.2005
| pmc = 1087395
| title = Haemophilus ducreyi Outer Membrane Determinants, Including DsrA, Define Two Clonal Populations
| pmid = 15784585
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- {{Cite journal
| doi = 10.1016/j.jmb.2004.10.006
| pmid = 15561140
| title = Cycling of the Sm-like Protein Hfq on the DsrA Small Regulatory RNA
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- {{Cite journal
| doi = 10.1038/nsmb858
| title = Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs
| pmc = 3071270
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| doi = 10.1128/JB.186.18.6179-6185.2004
| pmc = 515158
| title = The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli
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| pmc = 95095
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| year = 2000
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| title = DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription
| volume = 95
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| title = Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci
| volume = 95
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| pmid = 8670904
| year = 1996
| last1 = Sledjeski | first1 = D. D.
| last2 = Gupta | first2 = A.
| last3 = Gottesman | first3 = S.
| title = The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli
| volume = 15
| issue = 15
| pages = 3993–4000
| pmc = 452119
| journal = The EMBO Journal
| doi = 10.1002/j.1460-2075.1996.tb00773.x
}}
- {{cite journal|last=Geinguenaud|first=F|author2=Gesson, M |author3=Arluison, V |title=Thermodynamic aspects of the self-assembly of DsrA, a small noncoding RNA from Escherichia coli.|journal=Acta Biochimica Polonica|date=Jan 22, 2014|pmid=24455758|volume=61|issue=1|pages=179–184|doi=10.18388/abp.2014_1941|doi-access=free}}
- {{cite journal|last=Hämmerle|first=H|author2=Večerek, B |author3=Resch, A |author4= Bläsi, U |title=Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature.|journal=RNA Biology|date=Dec 1, 2013|volume=10|issue=12|pages=1834–1841|pmid=24448230 |doi=10.4161/rna.27100 |pmc=3917986}}
- {{cite journal|last1=Hämmerle|first1=H|last2=Večerek|first2=B|last3=Resch|first3=A|last4=Bläsi|first4=U|title=Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature.|journal=RNA Biology|date=Dec 1, 2013|volume=10|issue=12|pages=1834–1841|pmid=24448230|doi=10.4161/rna.27100|pmc=3917986}}
External links
- {{Rfam|id=RF00014|name=DsrA RNA}}
- [https://web.archive.org/web/20110707013004/http://ccb.bmi.ac.cn/srnatarbase/details.php?id=1 sRNATarBase page for DsrA interactions with hns]
- [https://web.archive.org/web/20110707013047/http://ccb.bmi.ac.cn/srnatarbase/details.php?id=2 sRNATarBase page for DsrA interactions with rbsD]
- [https://web.archive.org/web/20110707013108/http://ccb.bmi.ac.cn/srnatarbase/details.php?id=3 sRNATarBase page for DsrA interactions with argR]
- [https://web.archive.org/web/20110707013113/http://ccb.bmi.ac.cn/srnatarbase/details.php?id=4 sRNATarBase page for DsrA interactions with ilvI]
- [https://web.archive.org/web/20110707013118/http://ccb.bmi.ac.cn/srnatarbase/details.php?id=6 sRNATarBase page for DsrA interactions with rpoS]