RegulonDB RegulonDB 11.1: Operon Form
   

cspA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: cspA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: cspA
Gene(s): cspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): cspA gene expression is repressed by MetJ, which is a protein that appears to bind to a site upstream of this gene, but it is not known which of two promoters (cspAp1, cspAp2) affects MetJ Marincs F,2006.
The cspA gene was significantly upregulated in bacterial cells associated with lettuce roots in a microarray analysis Hou Z,2012.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Fang L., et al., 1997
[2] Hankins JS., et al., 2007
[3] Xia B., et al., 2002
Promoter
Name: cspAp1
+1: 3719889
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 160
Sequence: aatcataaatatgaaaaataattgttgcatcacccgccaatgcgtggcttaatgcacatcAacggtttgacgtacagacca
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [4] Etchegaray JP., et al., 1996
[5] Goldstein J., et al., 1990
[6] Huerta AM., et al., 2003
[7] Maciag A., et al., 2011
[8] Salgado H, et al., 2012
[9] Tanabe H., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: cacagaatctAAGATCCCTGCCATTTGGCGGGGATTTTtttatttgtt
Reference(s): [2] Hankins JS., et al., 2007
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis activator cspAp1 3719756 3719770 -126.0 taagtaagcaGTTGATGGAATAGACttttatccac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal Fis activator cspAp1 3719810 3719824 -72.0 ctgatgacagGACCGTTTTCCAACCgattaatcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal Fis activator cspAp1 3719893 3719907 12.0 cacatcaacgGTTTGACGTACAGACcattaaagca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
remote Fis activator cspAp1 3719968 3719982 87.0 ccctcgtagtGCACATTCCTTTAACgcttcaaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
remote Fis activator cspAp1 3720000 3720014 119.0 aatctgtaaaGCACGCCATATCGCCgaaaggcaca nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [11]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote H-NS repressor cspAp1 3719741 3719751 -143.5 aagccaacccGGCATTAAGTAagcagttgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
remote H-NS repressor cspAp1 3719779 3719789 -105.5 acttttatccACTTTATTGCTgtttacggtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal H-NS repressor cspAp1 3719823 3719840 -58.0 cgttttccaaCCGATTAATCATAAATATgaaaaataat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal H-NS repressor cspAp1 3719875 3719885 -9.5 ccaatgcgtgGCTTAATGCACatcaacggtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal H-NS repressor cspAp1 3719907 3719917 23.5 gacgtacagaCCATTAAAGCAgtgtagtaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition cspAp1 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [10]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [10] Brandi A., et al., 2016


Transcription unit       
Name: cspA
Gene(s): cspA   Genome Browser M3D Gene expression COLOMBOS
Note(s): cspA gene expression is repressed by MetJ, which is a protein that appears to bind to a site upstream of this gene, but it is not known which of two promoters (cspAp1, cspAp2) affects MetJ Marincs F,2006.
The cspA gene was significantly upregulated in bacterial cells associated with lettuce roots in a microarray analysis Hou Z,2012.
The mRNA produced by the cspA gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Fang L., et al., 1997
[2] Hankins JS., et al., 2007
[3] Xia B., et al., 2002
Promoter
Name: cspAp2
+1: 3719940
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 109
Sequence: atgcacatcaacggtttgacgtacagaccattaaagcagtgtagtaaggcaagtcccttcAagagttatcgttgatacccc
                     -35                     -10            +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Goldstein J., et al., 1990
[6] Huerta AM., et al., 2003
[9] Tanabe H., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: cacagaatctAAGATCCCTGCCATTTGGCGGGGATTTTtttatttgtt
Reference(s): [2] Hankins JS., et al., 2007


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.3 3720012 3720021 cgccatatcgCCGAAAGGCacacttaatt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg; thermoregulator
Strand: forward
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  cspA thermoregulator 493.4 3719889 3720316 aaugcacaucAACGGUUUGACGUACAGACCAUUAAAGCAGUGUAGUAAGGCAAGUCCCUUCAAGAGUUAUCGUUGAUACCCCUCGUAGUGCACAUUCCUUUAACGCUUCAAAAUCUGUAAAGCACGCCAUAUCGCCGAAAGGCACACUUAAUUAUUAAAGGUAAUACACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAGGCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGCCUGUAAUCUCUGCUUAAAAGCACAGAAUCUAAGAUCCCUGCCAUUUGGCGGGGAUUUUUUUauuuguuuuc
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Fang L., Jiang W., Bae W., Inouye M., 1997, Promoter-independent cold-shock induction of cspA and its derepression at 37 degrees C by mRNA stabilization., Mol Microbiol 23(2):355-64

 [2] 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

 [3] Xia B., Ke H., Jiang W., Inouye M., 2002, The Cold Box stem-loop proximal to the 5'-end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature., J Biol Chem 277(8):6005-11

 [4] Etchegaray JP., Jones PG., Inouye M., 1996, Differential thermoregulation of two highly homologous cold-shock genes, cspA and cspB, of Escherichia coli., Genes Cells 1(2):171-8

 [5] 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

 [6] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [7] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [8] 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.

 [9] 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

 [10] 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

 [11] Shao Y., Feldman-Cohen LS., Osuna R., 2008, Functional characterization of the Escherichia coli Fis-DNA binding sequence., J Mol Biol 376(3):771-85

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