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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 [3, 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 [9]. CspA acts as a positive transcription factor of at least two cold shock genes: hns [1, 4, 7] and gyrA [6]. cspA has been shown to negatively regulate its own expression as the result of attenuation of transcription [10]. A model of how CspA might affect the transcription of hns has been proposed [11].
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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], [TASES] [1], [2], [3], [4], [5]
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] [6]
  CspA activator gyrAp Sigma70 -88.0 -125.0 gyrA
2339542 2339548 [APIORCISFBSCS] [6]
  CspA activator gyrAp Sigma70 -60.0 -97.0 gyrA
2339514 2339520 [APIORCISFBSCS] [6]
  CspA activator hnsp Sigma70 nd nd hns nd nd [BPP] [1], [4], [7]

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


 [APPH] Assay of protein purified to homogeneity

 [IEP] Inferred from expression pattern

 [TASES] Traceable author statement to experimental support

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins


 [1] Brandi A., Pon CL., Gualerzi CO., 1994, Interaction of the main cold shock protein CS7.4 (CspA) of Escherichia coli with the promoter region of hns., Biochimie 76(10-11):1090-8

 [2] 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

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

 [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] 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

 [6] 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

 [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] Brandi A, Pon CL, 2012, Expression of Escherichia coli cspA during early exponential growth at 37 °C., Gene, 2012 Jan 25

 [10] Bae W, Jones PG, Inouye M, 1997, CspA, the major cold shock protein of Escherichia coli, negatively regulates its own gene expression., J Bacteriol, 1997 Nov

 [11] Johnston D, Tavano C, Wickner S, Trun N, 2006, Specificity of DNA binding and dimerization by CspE from Escherichia coli., J Biol Chem, 2006 Dec 29

 [12] Bae W, Phadtare S, Severinov K, Inouye M, 1999, Characterization of Escherichia coli cspE, whose product negatively regulates transcription of cspA, the gene for the major cold shock protein., Mol Microbiol, 1999 Mar

 [13] 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

 [14] Yamanaka K, Fang L, Inouye M, 1998, The CspA family in Escherichia coli: multiple gene duplication for stress adaptation., Mol Microbiol, 1998 Jan

 [15] Didier DK, Schiffenbauer J, Woulfe SL, Zacheis M, Schwartz BD, 1988, Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box., Proc Natl Acad Sci U S A, 1988 Oct

 [16] Schindelin H, Jiang W, Inouye M, Heinemann U, 1994, Crystal structure of CspA, the major cold shock protein of Escherichia coli., Proc Natl Acad Sci U S A, 1994 May 24

 [17] Newkirk K, Feng W, Jiang W, Tejero R, Emerson SD, Inouye M, Montelione GT, 1994, Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA., Proc Natl Acad Sci U S A, 1994 May 24

 [18] Feng W, Tejero R, Zimmerman DE, Inouye M, Montelione GT, 1998, Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site., Biochemistry, 1998 Aug 4

 [19] 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

 [20] 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

 [21] Brandi A, Spurio R, Gualerzi CO, Pon CL, 1999, Massive presence of the Escherichia coli 'major cold-shock protein' CspA under non-stress conditions., EMBO J, 1999 Mar 15

 [22] 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

 [23] 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

 [24] Jiang W, Fang L, Inouye M, 1996, The role of the 5'-end untranslated region of the mRNA for CspA, the major cold-shock protein of Escherichia coli, in cold-shock adaptation., J Bacteriol, 1996 Aug

 [25] Jiang W, Jones P, Inouye M, 1993, Chloramphenicol induces the transcription of the major cold shock gene of Escherichia coli, cspA., J Bacteriol, 1993 Sep

 [26] Etchegaray JP, Inouye M, 1999, CspA, CspB, and CspG, major cold shock proteins of Escherichia coli, are induced at low temperature under conditions that completely block protein synthesis., J Bacteriol, 1999 Mar

 [27] 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