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| | ==Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex== | | ==Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex== |
| - | <StructureSection load='2mf0' size='340' side='right'caption='[[2mf0]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2mf0' size='340' side='right'caption='[[2mf0]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2mf0]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Psef5 Psef5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MF0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2mf0]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens] and [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MF0 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2mf1|2mf1]]</div></td></tr> | + | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2mf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mf0 OCA], [https://pdbe.org/2mf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mf0 RCSB], [https://www.ebi.ac.uk/pdbsum/2mf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mf0 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsmE, csrA, PFL_2095 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2mf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mf0 OCA], [https://pdbe.org/2mf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mf0 RCSB], [https://www.ebi.ac.uk/pdbsum/2mf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mf0 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/Q4KEY0_PSEF5 Q4KEY0_PSEF5]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]
| + | [https://www.uniprot.org/uniprot/CSRA1_PSEPH CSRA1_PSEPH] A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).<ref>PMID:15601712</ref> <ref>PMID:16286659</ref> <ref>PMID:17704818</ref> <ref>PMID:23635605</ref> <ref>PMID:24561806</ref> <ref>PMID:24828038</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Psef5]] | + | [[Category: Pseudomonas fluorescens]] |
| - | [[Category: Allain, F H.T]] | + | [[Category: Pseudomonas protegens Pf-5]] |
| - | [[Category: Duss, O]] | + | [[Category: Allain FH-T]] |
| - | [[Category: Jeschke, G]] | + | [[Category: Duss O]] |
| - | [[Category: Michel, E]] | + | [[Category: Jeschke G]] |
| - | [[Category: Schubert, M]] | + | [[Category: Michel E]] |
| - | [[Category: Yulikov, M]] | + | [[Category: Schubert M]] |
| - | [[Category: Cooperativity]]
| + | [[Category: Yulikov M]] |
| - | [[Category: Electron paramagnetic resonance]]
| + | |
| - | [[Category: Homo-dimeric protein]]
| + | |
| - | [[Category: Large solution structure]]
| + | |
| - | [[Category: Messenger rna]]
| + | |
| - | [[Category: Multiple protein binding site]]
| + | |
| - | [[Category: Non-coding rna]]
| + | |
| - | [[Category: Protein sequestration]]
| + | |
| - | [[Category: Protein sponge]]
| + | |
| - | [[Category: Protein/rna]]
| + | |
| - | [[Category: Pseudomonas aeruginosa]]
| + | |
| - | [[Category: Ribosome binding site]]
| + | |
| - | [[Category: Rna binding protein-rna complex]]
| + | |
| - | [[Category: Rnase e cleave site]]
| + | |
| - | [[Category: Rnp assembly]]
| + | |
| - | [[Category: Translation activation]]
| + | |
| - | [[Category: Translation repressor protein]]
| + | |
| - | [[Category: Two conformation]]
| + | |
| Structural highlights
Function
CSRA1_PSEPH A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).[1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
MicroRNA and protein sequestration by non-coding RNAs (ncRNAs) has recently generated much interest. In the bacterial Csr/Rsm system, which is considered to be the most general global post-transcriptional regulatory system responsible for bacterial virulence, ncRNAs such as CsrB or RsmZ activate translation initiation by sequestering homodimeric CsrA-type proteins from the ribosome-binding site of a subset of messenger RNAs. However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level. Here we show for Pseudomonas fluorescens that RsmE protein dimers assemble sequentially, specifically and cooperatively onto the ncRNA RsmZ within a narrow affinity range. This assembly yields two different native ribonucleoprotein structures. Using a powerful combination of nuclear magnetic resonance and electron paramagnetic resonance spectroscopy we elucidate these 70-kilodalton solution structures, thereby revealing the molecular mechanism of the sequestration process and how RsmE binding protects the ncRNA from RNase E degradation. Overall, our findings suggest that RsmZ is well-tuned to sequester, store and release RsmE and therefore can be viewed as an ideal protein 'sponge'.
Structural basis of the non-coding RNA RsmZ acting as a protein sponge.,Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH Nature. 2014 May 29;509(7502):588-92. doi: 10.1038/nature13271. Epub 2014 May 14. PMID:24828038[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Reimmann C, Valverde C, Kay E, Haas D. Posttranscriptional repression of GacS/GacA-controlled genes by the RNA-binding protein RsmE acting together with RsmA in the biocontrol strain Pseudomonas fluorescens CHA0. J Bacteriol. 2005 Jan;187(1):276-85. PMID:15601712 doi:10.1128/JB.187.1.276-285.2005
- ↑ Kay E, Dubuis C, Haas D. Three small RNAs jointly ensure secondary metabolism and biocontrol in Pseudomonas fluorescens CHA0. Proc Natl Acad Sci U S A. 2005 Nov 22;102(47):17136-41. PMID:16286659 doi:10.1073/pnas.0505673102
- ↑ Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH. Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat Struct Mol Biol. 2007 Sep;14(9):807-13. Epub 2007 Aug 19. PMID:17704818 doi:10.1038/nsmb1285
- ↑ Lapouge K, Perozzo R, Iwaszkiewicz J, Bertelli C, Zoete V, Michielin O, Scapozza L, Haas D. RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family. RNA Biol. 2013 Jun;10(6):1031-41. PMID:23635605 doi:10.4161/rna.24771
- ↑ Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition. Nucleic Acids Res. 2014 Feb 21. PMID:24561806 doi:http://dx.doi.org/10.1093/nar/gku141
- ↑ Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014 May 29;509(7502):588-92. doi: 10.1038/nature13271. Epub 2014 May 14. PMID:24828038 doi:http://dx.doi.org/10.1038/nature13271
- ↑ Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014 May 29;509(7502):588-92. doi: 10.1038/nature13271. Epub 2014 May 14. PMID:24828038 doi:http://dx.doi.org/10.1038/nature13271
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