RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: spy
Gene(s): spy   Genome Browser M3D Gene expression COLOMBOS
Note(s): spy gene expression is induced separately by both copper and zinc metals through the CpxAR and BaeSR sensor response regulatory systems, respectively. BaeR can be the primary regulator and CpxR can enhance its function Yamamoto K,2008. 24999585 On the other hand, BaeR is the primary regulator of spy in the presence of the protein-unfolding agent ethanol 24999585
The expression of the gene spy is increased when colicin (at 30 ng/ml) is added to the medium 23421615. spy is also induced by indole Hirakawa H,2005. Raffa RG,2002.
Under conditions leading to NlpE outer membrane lipoprotein overexpression, the transcription of the spy gene is increased by CpxR Raivio TL,2013
The spy gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides 32385082.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Hagenmaier S., et al., 1997
[2] Nishino K., et al., 2005
Promoter
Name: spyp
+1: 1825688
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: acactttcattgttttaccgttgctctgattaattgacgctaaagtcagtaaagttaatcTcgtcaacacggcacgctact
                             -35                  -10       +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Hagenmaier S., et al., 1997
[3] Huerta AM., et al., 2003
[4] Yamamoto K., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: ttgagaagagAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTtttggctgaa
Reference(s): [1] Hagenmaier S., et al., 1997
TF binding sites (TFBSs)
[BaeR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal BaeR-phosphorylated activator spyp 1825765 1825784 -86.5 catcaaatttTCTTTTTTTCTCCATAATTGGcgcaaaagtg nd [AIBSCS], [APIORCISFBSCS], [BPP], [GEA] [2], [5]
remote BaeR-phosphorylated activator spyp 1825836 1825855 -157.5 accagtcatcCGGTATAGTTCTTCATAATCTctgcaaaatc nd [APIORCISFBSCS], [BPP], [IC] [5]
[CpxR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-phosphorylated1 activator spyp 1825731 1825745 -50.0 tgttttttacACTTTCATTGTTTTACcgttgctctg nd [APIORCISFBSCS], [BPP], [GEA] [4], [6], [7], [8]
Note(s): 1The consensus of this CpxR-binding site is not located in the same DNA strand as in the spyp promoter Yamamoto K,20063The consensus of this CpxR-binding site is not located in the same DNA strand as in the spyp promoter Yamamoto K,2006


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IC] Inferred by curator


Reference(s)    

 [1] Hagenmaier S., Stierhof YD., Henning U., 1997, A new periplasmic protein of Escherichia coli which is synthesized in spheroplasts but not in intact cells., J Bacteriol 179(6):2073-6

 [2] Nishino K., Honda T., Yamaguchi A., 2005, Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system., J Bacteriol 187(5):1763-72

 [3] 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

 [4] Yamamoto K., Ishihama A., 2006, Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli., Biosci Biotechnol Biochem 70(7):1688-95

 [5] Yamamoto K., Ogasawara H., Ishihama A., 2008, Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli., J Biotechnol 133(2):196-200

 [6] Raffa RG., Raivio TL., 2002, A third envelope stress signal transduction pathway in Escherichia coli., Mol Microbiol 45(6):1599-611

 [7] Raivio TL., Laird MW., Joly JC., Silhavy TJ., 2000, Tethering of CpxP to the inner membrane prevents spheroplast induction of the cpx envelope stress response., Mol Microbiol 37(5):1186-97

 [8] Raivio TL., Leblanc SK., Price NL., 2013, The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity., J Bacteriol 195(12):2755-67

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