RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: degP
Synonym(s): htrA
Gene(s): degP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the degP gene, encoding a protease, is affected by tetracycline antibiotic pressure. As tetracycline concentration increases, the gene expression also increases. The role of the induced protease could be degradation of porins to protect the cell against the antibiotic Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
The CpxR-dependent gene expression of degP is increased under the stress condition caused by the introduction of the R1-16 plasmid, which encodes the type IV secretion system (T4S machinery) in the cell Zahrl D,2006
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Fozo EM., et al., 2008
Promoter
Name: degPp
+1: 180845
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 39
Sequence: tttaccttttgcagaaactttagttcggaacttcaggctataaaacgaatctgaagaacaCagcaattttgcgttatctgt
                            -35                   -10       +1                   
Note(s): The degPp promoter was induced by zinc in a microarray analysis Yamamoto K,2005
The transcriptional start site of degPp was also determined by Rhodius VA,2005 and it was different by 1 bp from the one characterized by Yamamoto K,2005
It was suggested, from high-throughput screening of maps of transcriptional start sites (TSSs), that the TSS (180845) assigned for this promoter is an RNA processing site Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Dartigalongue C., et al., 2001
[3] Hiratsu K., et al., 1995
[4] Huerta AM., et al., 2003
[5] Lipinska B., et al., 1988
[6] Raina S., et al., 1995
[7] Rezuchova B., et al., 2001
[8] Rhodius VA., et al., 2005
[9] Yamamoto K., et al., 2005
[10] Yamamoto K., et al., 2006
TF binding sites (TFBSs)
[CpxR,+] 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 CpxR-phosphorylated activator degPp 180621 180622 -223.0 tcagtaaattAccgtcagatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [12]
proximal CpxR-phosphorylated activator degPp 180765 180783 -71.5 ccaggcttttGTAAAGACGAACAATAAATttttaccttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [10], [11], [12]
proximal CpxR-phosphorylated activator degPp 180781 180782 -63.0 cgaacaataaAtttttacctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11], [12]
[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
nd H-NS repressor degPp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [13]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

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

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

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

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence


Reference(s)    

 [1] Fozo EM., Kawano M., Fontaine F., Kaya Y., Mendieta KS., Jones KL., Ocampo A., Rudd KE., Storz G., 2008, Repression of small toxic protein synthesis by the Sib and OhsC small RNAs., Mol Microbiol 70(5):1076-93

 [2] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

 [3] Hiratsu K., Amemura M., Nashimoto H., Shinagawa H., Makino K., 1995, The rpoE gene of Escherichia coli, which encodes sigma E, is essential for bacterial growth at high temperature., J Bacteriol 177(10):2918-22

 [4] 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

 [5] Lipinska B., Sharma S., Georgopoulos C., 1988, Sequence analysis and regulation of the htrA gene of Escherichia coli: a sigma 32-independent mechanism of heat-inducible transcription., Nucleic Acids Res 16(21):10053-67

 [6] Raina S., Missiakas D., Georgopoulos C., 1995, The rpoE gene encoding the sigma E (sigma 24) heat shock sigma factor of Escherichia coli., EMBO J 14(5):1043-55

 [7] Rezuchova B., Kormanec J., 2001, A two-plasmid system for identification of promoters recognized by RNA polymerase containing extracytoplasmic stress response sigma(E) in Escherichia coli., J Microbiol Methods 45(2):103-11

 [8] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [9] Yamamoto K., Ishihama A., 2005, Transcriptional response of Escherichia coli to external zinc., J Bacteriol 187(18):6333-40

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

 [11] Danese PN., Snyder WB., Cosma CL., Davis LJ., Silhavy TJ., 1995, The Cpx two-component signal transduction pathway of Escherichia coli regulates transcription of the gene specifying the stress-inducible periplasmic protease, DegP., Genes Dev 9(4):387-98

 [12] Pogliano J., Lynch AS., Belin D., Lin EC., Beckwith J., 1997, Regulation of Escherichia coli cell envelope proteins involved in protein folding and degradation by the Cpx two-component system., Genes Dev 11(9):1169-82

 [13] Forns N., Juarez A., Madrid C., 2005, Osmoregulation of the HtrA (DegP) protease of Escherichia coli: an Hha-H-NS complex represses HtrA expression at low osmolarity., FEMS Microbiol Lett 251(1):75-80

RegulonDB