2mfc | pdb_00002mfc
Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL1)/RsmE(dimer) 2:1 complex
Structural highlights
FunctionCSRA1_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 PubMedThe 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
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