RegulonDB RegulonDB 11.0: Gene Form
   

cspA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yiaG cspA ysaE hokA mokA Fis Fis H-NS Fis H-NS H-NS Fis H-NS Fis H-NS ppGpp Cis-reg; thermoregulator terminator TSS_4161 TSS_4161 TSS_4160 TSS_4160 cspAp2 cspAp2 cspAp1 cspAp1

Gene      
Name: cspA    Texpresso search in the literature
Synonym(s): ECK3543, EG10166, b3556
Genome position(nucleotides): 3720049 --> 3720261
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.36
External database links:  
ASAP:
ABE-0011616
CGSC:
29540
ECHOBASE:
EB0164
ECOLIHUB:
cspA
OU-MICROARRAY:
b3556
STRING:
511145.b3556
COLOMBOS: cspA


Product      
Name: cold shock protein CspA
Synonym(s): CS7.4, CspA, DNA-binding transcriptional activator CspA, F10.6, major cold shock protein 7.4
Sequence: Get amino acid sequence Fasta Format
Regulator Family: Cold
Cellular location: cytosol
Molecular weight: 7.403
Isoelectric point: 5.715
Motif(s):
 
Type Positions Sequence Comment
2 -> 70 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL UniProt: Cold shock protein CspA.
5 -> 69 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS
7 -> 67 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV UniProt: CSD.

 

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 --> 3.1.2.2 - activator
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003697 - single-stranded DNA binding
GO:0003723 - RNA binding
GO:0003727 - single-stranded RNA binding
GO:0001072 - transcription antitermination factor activity, RNA binding
biological_process GO:0031564 - transcription antitermination
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0009409 - response to cold
GO:0010468 - regulation of gene expression
GO:0060567 - negative regulation of DNA-templated transcription, termination
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IEP] Inferred from expression pattern
Reference(s): [1] Jiang W., et al., 1997
[2] Jones PG., et al., 1987
[3] Kram KE., et al., 2020
[4] La Teana A., et al., 1991
[5] Podtelezhnikov AA., et al., 2009
[6] Sharan M., et al., 2017
External database links:  
ALPHAFOLD:
P0A9X9
DIP:
DIP-31862N
ECOCYC:
PD03695
ECOLIWIKI:
b3556
INTERPRO:
IPR002059
INTERPRO:
IPR012340
INTERPRO:
IPR012156
INTERPRO:
IPR019844
INTERPRO:
IPR011129
MODBASE:
P0A9X9
PDB:
3MEF
PDB:
2BH8
PDB:
1MJC
PDB:
2L15
PFAM:
PF00313
PRIDE:
P0A9X9
PRINTS:
PR00050
PRODB:
PRO_000022338
PROSITE:
PS00352
PROSITE:
PS51857
REFSEQ:
NP_418012
SMART:
SM00357
SMR:
P0A9X9
UNIPROT:
P0A9X9


Operon      
Name: cspA         
Operon arrangement:
Transcription unit        Promoter
cspA
cspA


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: H-NS


RNA cis-regulatory element    
Attenuation: Translational
   
Cis-reg; thermoregulator cspA thermoregulator
   
   


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_4160 3719942 forward nd [RS-EPT-CBR] [7]
  promoter TSS_4161 3720104 forward nd [RS-EPT-CBR] [7]


Evidence    

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



Reference(s)    

 [1] Jiang W., Hou Y., Inouye M., 1997, CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone., J Biol Chem 272(1):196-202

 [2] Jones PG., VanBogelen RA., Neidhardt FC., 1987, Induction of proteins in response to low temperature in Escherichia coli., J Bacteriol 169(5):2092-5

 [3] Kram KE., Henderson AL., Finkel SE., 2020, Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival., mSystems 5(4)

 [4] La Teana A., Brandi A., Falconi M., Spurio R., Pon CL., Gualerzi CO., 1991, Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS., Proc Natl Acad Sci U S A 88(23):10907-11

 [5] Podtelezhnikov AA., Wild DL., 2009, Reconstruction and stability of secondary structure elements in the context of protein structure prediction., Biophys J 96(11):4399-408

 [6] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96

 [7] 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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