RegulonDB RegulonDB 11.0: Gene Form
   

cspE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pagP crcB cspE CRP DinJ-YafQ Cis-reg; thermoregulator TSS_751 TSS_751 TSS_750 TSS_750 cspEp2 cspEp2 cspEp1 cspEp1

Gene      
Name: cspE    Texpresso search in the literature
Synonym(s): ECK0616, EG12179, b0623, gicA, msmC
Genome position(nucleotides): 657292 --> 657501
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 43.81
External database links:  
ASAP:
 ABE-0002142
CGSC:
 31528
ECHOBASE:
 EB2096
ECOLIHUB:
 cspE
OU-MICROARRAY:
 b0623
STRING:
 511145.b0623
COLOMBOS: cspE


Product      
Name: transcription antiterminator and regulator of RNA stability CspE
Synonym(s): CspE, GicA, MsmC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 7.463
Isoelectric point: 9.238
Motif(s):
 
Type Positions Sequence Comment
2 -> 69 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL UniProt: Cold shock-like protein CspE.
5 -> 68 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIA
6 -> 66 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV UniProt: CSD.
58 -> 58 A UniProt: In Ref. 2..

 
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
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:0008143 - poly(A) binding
GO:0042803 - protein homodimerization activity
GO:0001072 - transcription antitermination factor activity, RNA binding
biological_process GO:0031564 - transcription antitermination
GO:0010468 - regulation of gene expression
GO:0060567 - negative regulation of DNA-templated transcription, termination
Note(s): Note(s): ...[more].
Reference(s): [1] Hu Y., et al., 2012
[2] Kim MH., et al., 2015
[3] Kram KE., et al., 2020
[4] Longo F., et al., 2016
[5] Moore JM., et al., 2015
[6] Phadtare S., et al., 2003
[7] Shenhar Y., et al., 2012
[8] Stein EM., et al., 2020
[9] Uppal S., et al., 2011
External database links:  
ALPHAFOLD:
 P0A972
DIP:
 DIP-47834N
ECOCYC:
 EG12179-MONOMER
ECOLIWIKI:
 b0623
INTERPRO:
 IPR019844
INTERPRO:
 IPR002059
INTERPRO:
 IPR012156
INTERPRO:
 IPR012340
INTERPRO:
 IPR011129
MODBASE:
 P0A972
PFAM:
 PF00313
PRIDE:
 P0A972
PRINTS:
 PR00050
PRODB:
 PRO_000022342
PROSITE:
 PS00352
PROSITE:
 PS51857
REFSEQ:
 NP_415156
SMART:
 SM00357
SMR:
 P0A972
SWISSMODEL:
 P0A972
UNIPROT:
 P0A972


Operon      
Name: cspE         
Operon arrangement:
Transcription unit        Promoter
cspE
cspE


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: DinJ-YafQ


RNA cis-regulatory element    
   
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_750 657301 forward nd [RS-EPT-CBR] [10]
  promoter TSS_751 657375 forward nd [RS-EPT-CBR] [10]


Evidence    

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


Reference(s)    

 [1] Hu Y., Benedik MJ., Wood TK., 2012, Antitoxin DinJ influences the general stress response through transcript stabilizer CspE., Environ Microbiol 14(3):669-79

 [2] Kim MH., Imai R., 2015, Determination of RNA chaperone activity using an Escherichia coli mutant., Methods Mol Biol 1259:117-23

 [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] Longo F., Motta S., Mauri P., Landini P., Rossi E., 2016, Interplay of the modified nucleotide phosphoadenosine 5'-phosphosulfate (PAPS) with global regulatory proteins in Escherichia coli: modulation of cyclic AMP (cAMP)-dependent gene expression and interaction with the HupA regulatory protein., Chem Biol Interact 259(Pt A):39-47

 [5] Moore JM., Magnan D., Mojica AK., Nunez MA., Bates D., Rosenberg SM., Hastings PJ., 2015, Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in Starving Escherichia coli., Genetics 201(4):1349-62

 [6] Phadtare S., Severinov K., Inouye M., 2003, Assay of transcription antitermination by proteins of the CspA family., Methods Enzymol 371:460-71

 [7] Shenhar Y., Biran D., Ron EZ., 2012, Resistance to environmental stress requires the RNA chaperones CspC and CspE., Environ Microbiol Rep 4(5):532-9

 [8] Stein EM., Kwiatkowska J., Basczok MM., Gravel CM., Berry KE., Olejniczak M., 2020, Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein., Nucleic Acids Res 48(13):7502-7519

 [9] Uppal S., Maurya SR., Hire RS., Jawali N., 2011, Cyclic AMP Receptor Protein Regulates cspE, an Early Cold-Inducible Gene, in Escherichia coli., J Bacteriol 193(22):6142-51

 [10] 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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