RegulonDB RegulonDB 10.9: Gene Form
   

csqR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yihV csqR yihX yihY CRP terminator yihXp yihXp TSS_4579 TSS_4579 csqRp csqRp

Gene      
Name: csqR    Texpresso search in the literature
Synonym(s): ECK3877, EG11849, b3884, yihW
Genome position(nucleotides): 4074669 --> 4075454 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.42
External database links:  
ASAP:
ABE-0012683
ECHOBASE:
EB1795
ECOLIHUB:
yihW
OU-MICROARRAY:
b3884
STRING:
511145.b3884
COLOMBOS: csqR


Product      
Name: DNA-binding transcriptional dual regulator CsqR
Synonym(s): CsqR, YihW
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 28.507
Isoelectric point: 5.906
Motif(s):
 
Type Positions Sequence
11 -> 66 RHDQLLMLIAERGYMNIDELANLLDVSTQTVRRDIRKLSEQGLITRHHGGAGRASS
79 -> 237 QTEEKKAIAEAVADYIPDGSTIFITIGTTVEHVARALLNHNHLRIITNSLRVAHILYHNPRFEVMVPGGTLRSHNSGIIGPSAASFVADFRADYLVTSVGAIESDGALMEFDVNEANVVKTMMAHARNILLVADHTKYHASAAVEIGNVAQVTALFTDE
8 -> 63 GNPRHDQLLMLIAERGYMNIDELANLLDVSTQTVRRDIRKLSEQGLITRHHGGAGR
25 -> 44 MNIDELANLLDVSTQTVRRD

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.2 - regulon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:2000143 - negative regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
Reference(s): [1] Kaznadzey A., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
[4] Shimada T., et al., 2019
External database links:  
DIP:
DIP-12504N
ECOCYC:
EG11849-MONOMER
ECOLIWIKI:
b3884
INTERPRO:
IPR011991
INTERPRO:
IPR037171
INTERPRO:
IPR036390
INTERPRO:
IPR036388
INTERPRO:
IPR018356
INTERPRO:
IPR014036
INTERPRO:
IPR001034
MODBASE:
P32144
PFAM:
PF08220
PFAM:
PF00455
PRIDE:
P32144
PRINTS:
PR00037
PROSITE:
PS51000
PROSITE:
PS00894
REFSEQ:
NP_418320
SMART:
SM00420
UNIPROT:
P32144


Operon      
Name: yihV-csqR         
Operon arrangement:
Transcription unit        Promoter
yihV-csqR
yihW


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: CRP, CsqR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4579 4075529 forward nd [RS-EPT-CBR] [5]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Kaznadzey A., Shelyakin P., Belousova E., Eremina A., Shvyreva U., Bykova D., Emelianenko V., Korosteleva A., Tutukina M., Gelfand MS., 2018, The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation., Sci Rep 8(1):3177

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [4] Shimada T., Yamamoto K., Nakano M., Watanabe H., Schleheck D., Ishihama A., 2019, Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12., Microbiology 165(1):78-89

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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