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CspA DNA-binding transcriptional activator

Synonyms: CspA
The "Cold shock protein A," CspA, is a major cold shock protein and was shown to be detected only during early-log-phase growth at 37°C and during log phase after a shift from 37°C to 10°C [2, 8]. However, studies have shown that although the expression of cspA is reduced during stationary phase, cspA mRNA and CspA are detectable during all growth phases []. CspA acts as a positive transcription factor of at least two cold shock genes: hns [4, 7] and gyrA [9]. cspA has been shown to negatively regulate its own expression as the result of attenuation of transcription []. A model of how CspA might affect the transcription of hns has been proposed [].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CspA Functional   [APPH], [IEP] [1], [2], [3], [4], [5], [6]
Evolutionary Family: Cold
Connectivity class: Local Regulator
Gene name: cspA
  Genome position: 3720049-3720261
  Length: 213 bp / 70 aa
Operon name: cspA
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) gyrA, hns
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
DNA replication (1)
Transcription related (1)
nucleoproteins, basic proteins (1)
activator (1)
repressor (1)
Regulated operon(s) gyrA, hns
First gene in the operon(s) gyrA, hns
Simple and complex regulons CRP,CspA,Fis
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

Transcription factor binding sites (TFBSs) arrangements

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  CspA activator gyrAp Sigma70 -108.0 -145.0 gyrA
2339562 2339568 [APIORCISFBSCS]
  CspA activator gyrAp Sigma70 -88.0 -125.0 gyrA
2339542 2339548 [APIORCISFBSCS]
  CspA activator gyrAp Sigma70 -60.0 -97.0 gyrA
2339514 2339520 [APIORCISFBSCS]
  CspA activator hnsp Sigma70 nd nd hns nd nd [BPP], [GEA], [IGI] [7]

Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


 [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] Giangrossi M., Gualerzi CO., Pon CL., 2001, Mutagenesis of the downstream region of the Escherichia coli hns promoter., Biochimie 83(2):251-9

 [8] Goldstein J., Pollitt NS., Inouye M., 1990, Major cold shock protein of Escherichia coli., Proc Natl Acad Sci U S A 87(1):283-7

 [9] Jones PG., Krah R., Tafuri SR., Wolffe AP., 1992, DNA gyrase, CS7.4, and the cold shock response in Escherichia coli., J Bacteriol 174(18):5798-802

 [10] Zere TR., Vakulskas CA., Leng Y., Pannuri A., Potts AH., Dias R., Tang D., Kolaczkowski B., Georgellis D., Ahmer BM., Romeo T., 2015, Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems., PLoS One 10(12):e0145035

 [11] Brandi A., Giangrossi M., Giuliodori AM., Falconi M., 2016, An Interplay among FIS, H-NS, and Guanosine Tetraphosphate Modulates Transcription of the Escherichia coli cspA Gene under Physiological Growth Conditions., Front Mol Biosci 3:19

 [12] Tanabe H., Goldstein J., Yang M., Inouye M., 1992, Identification of the promoter region of the Escherichia coli major cold shock gene, cspA., J Bacteriol 174(12):3867-73

 [13] Hankins JS., Zappavigna C., Prud'homme-Genereux A., Mackie GA., 2007, Role of RNA structure and susceptibility to RNase E in regulation of a cold shock mRNA, cspA mRNA., J Bacteriol 189(12):4353-8

 [14] Ivancic T., Jamnik P., Stopar D., 2013, Cold shock CspA and CspB protein production during periodic temperature cycling in Escherichia coli., BMC Res Notes 6:248

 [15] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15