CSRD_ECOLI
ID CSRD_ECOLI Reviewed; 646 AA.
AC P13518; Q2M8W2;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=RNase E specificity factor CsrD;
DE AltName: Full=Regulator of CsrB and CsrC decay CsrD;
GN Name=csrD; Synonyms=yhdA; OrderedLocusNames=b3252, JW3221;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 545-646.
RC STRAIN=K12;
RX PubMed=3049542; DOI=10.1128/jb.170.10.4619-4624.1988;
RA Doi M., Wachi M., Ishino F., Tomioka S., Ito M., Sakagami Y., Suzuki A.,
RA Matsuhashi M.;
RT "Determinations of the DNA sequence of the mreB gene and of the gene
RT products of the mre region that function in formation of the rod shape of
RT Escherichia coli cells.";
RL J. Bacteriol. 170:4619-4624(1988).
RN [4]
RP FUNCTION IN REGULATION OF CARBON STORAGE REGULATION SYSTEM, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / MG1655 / CF7789;
RX PubMed=17064377; DOI=10.1111/j.1574-6968.2006.00457.x;
RA Jonas K., Tomenius H., Romling U., Georgellis D., Melefors O.;
RT "Identification of YhdA as a regulator of the Escherichia coli carbon
RT storage regulation system.";
RL FEMS Microbiol. Lett. 264:232-237(2006).
RN [5]
RP FUNCTION, MUTAGENESIS OF LEU-584, DOMAIN EAL AND GGDEF, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / MG1655 / CF7789;
RX PubMed=16980588; DOI=10.1101/gad.1461606;
RA Suzuki K., Babitzke P., Kushner S.R., Romeo T.;
RT "Identification of a novel regulatory protein (CsrD) that targets the
RT global regulatory RNAs CsrB and CsrC for degradation by RNase E.";
RL Genes Dev. 20:2605-2617(2006).
RN [6]
RP FUNCTION IN CURLI EXPRESSION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=19332833; DOI=10.1099/mic.0.024257-0;
RA Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N.,
RA Hengge R.;
RT "Gene expression patterns and differential input into curli fimbriae
RT regulation of all GGDEF/EAL domain proteins in Escherichia coli.";
RL Microbiology 155:1318-1331(2009).
CC -!- FUNCTION: Serves as a specificity factor required for RNase E-mediated
CC decay of the small global regulatory RNAs CsrB and CsrC, it is probably
CC not a nuclease. Nor does its activity involve c-di-GMP, despite its
CC domain composition. Positively modulates motility gene expression, is
CC also required for curli expression. {ECO:0000269|PubMed:16980588,
CC ECO:0000269|PubMed:17064377, ECO:0000269|PubMed:19332833}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Multi-pass membrane
CC protein {ECO:0000305}.
CC -!- INDUCTION: Expressed at low levels at both 28 and 37 degrees Celsius.
CC {ECO:0000269|PubMed:19332833}.
CC -!- DOMAIN: Removal of the transmembrane regions (residues 1-156) has no
CC effect on csrB translation, however removal of either the HAMP-like
CC region, EAL or GGDEF domains obviates the activity of CsrD.
CC {ECO:0000269|PubMed:16980588}.
CC -!- DISRUPTION PHENOTYPE: Dramatically stabilizes CsrB and CsrC RNAs, small
CC RNAs that sequester the global carbon storage regulator CsrA; also
CC decreased transcription of CsrB/C (PubMed:16980588). Decreased biofilm
CC formation, decreased expression of DgcC, a probable diguanylate cyclase
CC and of the curli regulator CsgD. Decreased expression of the curlin
CC subunit CsgB, decreased curli expression at 28 degrees Celsius
CC (PubMed:19332833). {ECO:0000269|PubMed:16980588,
CC ECO:0000269|PubMed:17064377, ECO:0000269|PubMed:19332833}.
CC -!- CAUTION: Although this protein contains both EAL and GGDEF domains it
CC is unlikely to have either c-di-GMP phosphodiesterase or diguanylate
CC cyclase activities as amino acids known to be important to these
CC activities are not conserved. {ECO:0000305}.
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DR EMBL; U18997; AAA58055.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76284.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77294.1; -; Genomic_DNA.
DR EMBL; M22055; AAA83890.1; -; Genomic_DNA.
DR PIR; F65117; QQECE5.
DR RefSeq; NP_417718.1; NC_000913.3.
DR RefSeq; WP_001241469.1; NZ_SSZK01000034.1.
DR AlphaFoldDB; P13518; -.
DR SMR; P13518; -.
DR BioGRID; 4261943; 11.
DR DIP; DIP-12292N; -.
DR IntAct; P13518; 1.
DR STRING; 511145.b3252; -.
DR jPOST; P13518; -.
DR PaxDb; P13518; -.
DR PRIDE; P13518; -.
DR EnsemblBacteria; AAC76284; AAC76284; b3252.
DR EnsemblBacteria; BAE77294; BAE77294; BAE77294.
DR GeneID; 947702; -.
DR KEGG; ecj:JW3221; -.
DR KEGG; eco:b3252; -.
DR PATRIC; fig|1411691.4.peg.3477; -.
DR EchoBASE; EB0018; -.
DR eggNOG; COG2199; Bacteria.
DR eggNOG; COG2200; Bacteria.
DR HOGENOM; CLU_028330_0_0_6; -.
DR InParanoid; P13518; -.
DR OMA; CQYIGRL; -.
DR PhylomeDB; P13518; -.
DR BioCyc; EcoCyc:EG10018-MON; -.
DR PRO; PR:P13518; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0034661; P:ncRNA catabolic process; IMP:EcoCyc.
DR GO; GO:0051252; P:regulation of RNA metabolic process; IMP:EcoCyc.
DR CDD; cd01948; EAL; 1.
DR CDD; cd01949; GGDEF; 1.
DR Gene3D; 3.20.20.450; -; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR001633; EAL_dom.
DR InterPro; IPR035919; EAL_sf.
DR InterPro; IPR033423; GAPES4.
DR InterPro; IPR000160; GGDEF_dom.
DR InterPro; IPR029787; Nucleotide_cyclase.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR Pfam; PF00563; EAL; 1.
DR Pfam; PF17157; GAPES4; 1.
DR Pfam; PF00990; GGDEF; 1.
DR SMART; SM00052; EAL; 1.
DR SMART; SM00267; GGDEF; 1.
DR SUPFAM; SSF141868; SSF141868; 1.
DR SUPFAM; SSF55073; SSF55073; 1.
DR TIGRFAMs; TIGR00254; GGDEF; 1.
DR PROSITE; PS50883; EAL; 1.
DR PROSITE; PS50887; GGDEF; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Coiled coil; Membrane; Reference proteome; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..646
FT /note="RNase E specificity factor CsrD"
FT /id="PRO_0000169492"
FT TRANSMEM 10..30
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 135..155
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 254..387
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT DOMAIN 396..644
FT /note="EAL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
FT REGION 152..219
FT /note="HAMP-like"
FT COILED 194..224
FT /evidence="ECO:0000255"
FT MUTAGEN 584
FT /note="L->A: Decreased transcription of csrB."
FT /evidence="ECO:0000269|PubMed:16980588"
SQ SEQUENCE 646 AA; 73339 MW; 0387E011BC4D06B8 CRC64;
MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV
LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR
LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER
GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN
QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL
LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT
EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR TLIEQMLSRG GPRLYQKPAV
TREGQVHHRE LMCRIFDGNE EVSSAEYMPM VLQFGLSEEY DRLQISRLIP LLRYWPEENL
AIQVTVESLI RPRFQRWLRD TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG
VRVAVNQAGL TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV
YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV
