CSRA1_PSEPH
ID CSRA1_PSEPH Reviewed; 64 AA.
AC P0DPC3;
DT 20-DEC-2017, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2017, sequence version 1.
DT 25-MAY-2022, entry version 18.
DE RecName: Full=Translational regulator CsrA1 {ECO:0000255|HAMAP-Rule:MF_00167, ECO:0000305};
DE AltName: Full=Carbon storage regulator 1 {ECO:0000255|HAMAP-Rule:MF_00167};
DE AltName: Full=Regulator of secondary metabolites RsmE {ECO:0000303|PubMed:15601712};
GN Name=csrA1 {ECO:0000255|HAMAP-Rule:MF_00167, ECO:0000305};
GN Synonyms=rsmE {ECO:0000303|PubMed:15601712};
OS Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CFBP 6595 / CHA0).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=1124983;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION, DISRUPTION
RP PHENOTYPE, AND RNA-BINDING.
RC STRAIN=DSM 19095 / LMG 27888 / CFBP 6595 / CHA0;
RX PubMed=15601712; DOI=10.1128/jb.187.1.276-285.2005;
RA Reimmann C., Valverde C., Kay E., Haas D.;
RT "Posttranscriptional repression of GacS/GacA-controlled genes by the RNA-
RT binding protein RsmE acting together with RsmA in the biocontrol strain
RT Pseudomonas fluorescens CHA0.";
RL J. Bacteriol. 187:276-285(2005).
RN [2]
RP FUNCTION, AND RNA-BINDING.
RC STRAIN=DSM 19095 / LMG 27888 / CFBP 6595 / CHA0;
RX PubMed=16286659; DOI=10.1073/pnas.0505673102;
RA Kay E., Dubuis C., Haas D.;
RT "Three small RNAs jointly ensure secondary metabolism and biocontrol in
RT Pseudomonas fluorescens CHA0.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:17136-17141(2005).
RN [3]
RP FUNCTION, SUBUNIT, AND RNA-BINDING.
RX PubMed=23635605; DOI=10.4161/rna.24771;
RA Lapouge K., Perozzo R., Iwaszkiewicz J., Bertelli C., Zoete V.,
RA Michielin O., Scapozza L., Haas D.;
RT "RNA pentaloop structures as effective targets of regulators belonging to
RT the RsmA/CsrA protein family.";
RL RNA Biol. 10:1031-1041(2013).
RN [4]
RP REVIEW.
RX PubMed=25833324; DOI=10.1128/mmbr.00052-14;
RA Vakulskas C.A., Potts A.H., Babitzke P., Ahmer B.M., Romeo T.;
RT "Regulation of bacterial virulence by Csr (Rsm) systems.";
RL Microbiol. Mol. Biol. Rev. 79:193-224(2015).
RN [5] {ECO:0007744|PDB:2JPP}
RP STRUCTURE BY NMR IN COMPLEX WITH MRNA 5' UTR, FUNCTION, SUBUNIT, DOMAIN,
RP MUTAGENESIS OF LEU-4; ARG-6 AND ARG-44, AND RNA-BINDING.
RC STRAIN=DSM 19095 / LMG 27888 / CFBP 6595 / CHA0;
RX PubMed=17704818; DOI=10.1038/nsmb1285;
RA Schubert M., Lapouge K., Duss O., Oberstrass F.C., Jelesarov I., Haas D.,
RA Allain F.H.;
RT "Molecular basis of messenger RNA recognition by the specific bacterial
RT repressing clamp RsmA/CsrA.";
RL Nat. Struct. Mol. Biol. 14:807-813(2007).
RN [6] {ECO:0007744|PDB:2MF0, ECO:0007744|PDB:2MF1}
RP STRUCTURE BY NMR OF 1-59 IN COMPLEX WITH RSMZ RNA, FUNCTION, SUBUNIT, AND
RP RNA-BINDING.
RC STRAIN=DSM 19095 / LMG 27888 / CFBP 6595 / CHA0;
RX PubMed=24828038; DOI=10.1038/nature13271;
RA Duss O., Michel E., Yulikov M., Schubert M., Jeschke G., Allain F.H.;
RT "Structural basis of the non-coding RNA RsmZ acting as a protein sponge.";
RL Nature 509:588-592(2014).
RN [7] {ECO:0007744|PDB:2MFC, ECO:0007744|PDB:2MFE, ECO:0007744|PDB:2MFF, ECO:0007744|PDB:2MFG, ECO:0007744|PDB:2MFH}
RP STRUCTURE BY NMR OF 1-59 IN COMPLEX WITH 5 RSMZ RNA FRAGMENTS, FUNCTION,
RP SUBUNIT, DOMAIN, AND RNA-BINDING.
RC STRAIN=DSM 19095 / LMG 27888 / CFBP 6595 / CHA0;
RX PubMed=24561806; DOI=10.1093/nar/gku141;
RA Duss O., Michel E., Diarra dit Konte N., Schubert M., Allain F.H.;
RT "Molecular basis for the wide range of affinity found in Csr/Rsm protein-
RT RNA recognition.";
RL Nucleic Acids Res. 42:5332-5346(2014).
CC -!- FUNCTION: A translational regulator that binds mRNA to regulate
CC translation initiation and/or mRNA stability (PubMed:17704818,
CC PubMed:23635605). Post-transcriptionally represses the expression of
CC genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds
CC the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer
CC and each dimer could bind the same mRNA twice (PubMed:17704818).
CC Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the
CC Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome
CC binding (PubMed:17704818, PubMed:24561806, PubMed:23635605).
CC Overexpression represses target protein expression; mutating
CC nucleotides in the 5' UTR abolishes repression in vivo
CC (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs
CC (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures
CC with multiple GGA sequences in loops to which the CsrA proteins bind
CC (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX,
CC RsmY or RsmZ titrates the protein so that it can no longer bind mRNA
CC and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can
CC bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA
CC sequences in RsmZ in a defined order (PubMed:24828038,
CC PubMed:24561806). Required for optimal expression and stability of
CC sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four
CC CsrA1 dimers maximally protect RsmZ from RNase activity
CC (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no
CC detectable phenotype, but a double rsmY-rsmZ deletion has a marked
CC decrease in production of secondary metabolites HCN, exoprotease AprA,
CC antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and
CC protects cucumber plants from fungal infection less well than wild-
CC type; the triple sRNA deletion has even stronger loss of these
CC phenotypes (PubMed:16286659). {ECO:0000269|PubMed:15601712,
CC ECO:0000269|PubMed:16286659, ECO:0000269|PubMed:17704818,
CC ECO:0000269|PubMed:23635605, ECO:0000269|PubMed:24561806,
CC ECO:0000269|PubMed:24828038}.
CC -!- SUBUNIT: Homodimer (PubMed:23635605, PubMed:17704818, PubMed:24828038,
CC PubMed:24561806). The beta-strands of each monomer intercalate to form
CC a hydrophobic core while the alpha-helices form wings that extend away
CC from the core (PubMed:17704818, PubMed:24828038, PubMed:24561806).
CC {ECO:0000269|PubMed:17704818, ECO:0000269|PubMed:23635605,
CC ECO:0000269|PubMed:24561806, ECO:0000269|PubMed:24828038}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00167}.
CC -!- INDUCTION: Expressed at low levels during exponential growth,
CC considerably more protein expressed in stationary phase (at protein
CC level) (PubMed:15601712). Positively controlled by GacA and negatively
CC regulated by CsrA1 and CsrA2 (PubMed:15601712).
CC {ECO:0000269|PubMed:15601712}.
CC -!- DOMAIN: Residues in the N-terminus (2-4) and C-terminus (37-44) help
CC recognize the GGA loop in a mRNA stem-loop; recognition mostly occurs
CC via the protein main chain carbonyl oxygens and amides
CC (PubMed:17704818). Similar interactions occur with fragments of sRNA
CC RsmZ; the binding affinity for GGA-containing RsmZ fragments can vary
CC from 10 nM to 3 mM depending on the sequence and structural context
CC (PubMed:24561806). {ECO:0000269|PubMed:17704818,
CC ECO:0000269|PubMed:24561806}.
CC -!- DISRUPTION PHENOTYPE: Increased expression of genes controlled by
CC GacA/GacS (aprA, hcnA, phlA), partially suppresses a gacS deletion
CC mutant (PubMed:15601712). Double csrA1-csrA2 deletion mutants fully
CC suppress the requirement for GacA/GacS in control of its regulon
CC (PubMed:15601712). Decreased expression and stability of RsmY and RsmZ
CC sRNAs (PubMed:15601712). {ECO:0000269|PubMed:15601712}.
CC -!- SIMILARITY: Belongs to the CsrA/RsmA family. {ECO:0000255|HAMAP-
CC Rule:MF_00167}.
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DR EMBL; AY547272; AAT27429.1; -; Genomic_DNA.
DR RefSeq; WP_007920550.1; NZ_LS999205.1.
DR PDB; 2JPP; NMR; -; A/B=1-64.
DR PDB; 2MF0; NMR; -; A/B/C/D/E/F=1-59.
DR PDB; 2MF1; NMR; -; A/B/C/D/E/F=1-59.
DR PDB; 2MFC; NMR; -; A/C=1-59.
DR PDB; 2MFE; NMR; -; A/C=1-59.
DR PDB; 2MFF; NMR; -; A/C=1-59.
DR PDB; 2MFG; NMR; -; A/C=1-59.
DR PDB; 2MFH; NMR; -; A/C=1-59.
DR PDBsum; 2JPP; -.
DR PDBsum; 2MF0; -.
DR PDBsum; 2MF1; -.
DR PDBsum; 2MFC; -.
DR PDBsum; 2MFE; -.
DR PDBsum; 2MFF; -.
DR PDBsum; 2MFG; -.
DR PDBsum; 2MFH; -.
DR AlphaFoldDB; P0DPC3; -.
DR SMR; P0DPC3; -.
DR STRING; 1124983.PFLCHA0_c21410; -.
DR GeneID; 61649724; -.
DR eggNOG; COG1551; Bacteria.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0048027; F:mRNA 5'-UTR binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:InterPro.
DR GO; GO:0045947; P:negative regulation of translational initiation; IEA:UniProtKB-UniRule.
DR GO; GO:0045948; P:positive regulation of translational initiation; IEA:UniProtKB-UniRule.
DR GO; GO:0006109; P:regulation of carbohydrate metabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 2.60.40.4380; -; 1.
DR HAMAP; MF_00167; CsrA; 1.
DR InterPro; IPR003751; CsrA.
DR InterPro; IPR036107; CsrA_sf.
DR PANTHER; PTHR34984; PTHR34984; 1.
DR Pfam; PF02599; CsrA; 1.
DR SUPFAM; SSF117130; SSF117130; 1.
DR TIGRFAMs; TIGR00202; csrA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; Cytoplasm; Repressor; RNA-binding;
KW Translation regulation.
FT CHAIN 1..64
FT /note="Translational regulator CsrA1"
FT /id="PRO_0000442648"
FT REGION 1..7
FT /note="Contacts 5' UTR of mRNA"
FT /evidence="ECO:0000269|PubMed:17704818"
FT REGION 28..31
FT /note="Contacts 5' UTR of mRNA"
FT /evidence="ECO:0000269|PubMed:17704818"
FT REGION 37..44
FT /note="Contacts 5' UTR of mRNA"
FT /evidence="ECO:0000269|PubMed:17704818"
FT REGION 47..50
FT /note="Contacts 5' UTR of mRNA"
FT /evidence="ECO:0000269|PubMed:17704818"
FT MUTAGEN 4
FT /note="L->A: Partial loss of repression of hcnA in vivo,
FT decreased affinity for mRNA."
FT /evidence="ECO:0000269|PubMed:17704818"
FT MUTAGEN 6
FT /note="R->A: Complete loss of repression of hcnA in vivo."
FT /evidence="ECO:0000269|PubMed:17704818"
FT MUTAGEN 44
FT /note="R->A: Partial loss of repression of hcnA in vivo,
FT decreased affinity for mRNA."
FT /evidence="ECO:0000269|PubMed:17704818"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2JPP"
FT STRAND 11..14
FT /evidence="ECO:0007829|PDB:2JPP"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:2JPP"
FT STRAND 18..26
FT /evidence="ECO:0007829|PDB:2JPP"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:2JPP"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2JPP"
FT HELIX 45..51
FT /evidence="ECO:0007829|PDB:2JPP"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:2MF0"
SQ SEQUENCE 64 AA; 7010 MW; 858BEEE88ABF0FB8 CRC64;
MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPDK
RETP
