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| | ==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL3)/RsmE(dimer) 2:1 complex== | | ==Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL3)/RsmE(dimer) 2:1 complex== |
| - | <StructureSection load='2mff' size='340' side='right'caption='[[2mff]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2mff' size='340' side='right'caption='[[2mff]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2mff]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2mff]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MFF 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;'>[[2mfc|2mfc]], [[2mfe|2mfe]], [[2mfg|2mfg]], [[2mfh|2mfh]]</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=2mff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mff OCA], [https://pdbe.org/2mff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mff RCSB], [https://www.ebi.ac.uk/pdbsum/2mff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mff ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsmE, csrA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=2mff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mff OCA], [https://pdbe.org/2mff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mff RCSB], [https://www.ebi.ac.uk/pdbsum/2mff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mff ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/Q5MXB2_PSEFL Q5MXB2_PSEFL]] 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens liquefaciens flugge 1886]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Allain, F H.T]] | + | [[Category: Pseudomonas fluorescens]] |
| - | [[Category: Duss, O]] | + | [[Category: Allain FH-T]] |
| - | [[Category: Konte, N Diarra Dit]] | + | [[Category: Diarra Dit Konte N]] |
| - | [[Category: Michel, E]] | + | [[Category: Duss O]] |
| - | [[Category: Schubert, M]] | + | [[Category: Michel E]] |
| - | [[Category: Bacterial protein]] | + | [[Category: Schubert M]] |
| - | [[Category: Csra]]
| + | |
| - | [[Category: Csrb]]
| + | |
| - | [[Category: Messenger rna]]
| + | |
| - | [[Category: Modulation of binding affinity]]
| + | |
| - | [[Category: Molecular mimicry]]
| + | |
| - | [[Category: Non-coding rna]]
| + | |
| - | [[Category: Protein sequestration]]
| + | |
| - | [[Category: Pseudomonas aeruginosa]]
| + | |
| - | [[Category: Rna-binding protein]]
| + | |
| - | [[Category: Rsma]]
| + | |
| - | [[Category: Rsme]]
| + | |
| - | [[Category: Rsmz]]
| + | |
| - | [[Category: Srna]]
| + | |
| - | [[Category: Translation activation]]
| + | |
| - | [[Category: Translation repressor protein]]
| + | |
| - | [[Category: Translation-rna complex]]
| + | |
| 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
The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude ( approximately 10 nM to approximately 3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.
Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.,Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH Nucleic Acids Res. 2014 Feb 21. PMID:24561806[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, 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
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