RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: cadBA
Gene(s): cadA, cadB   Genome Browser M3D Gene expression COLOMBOS
Note(s): In RegulonDB, there was one transcription unit, cadCBA. Current information suggests that there are two transcription units, cadC and cadBA.
Regulation has been described Auger EA, Redding KE, Plumb T, Childs LC, Meng SY, Bennett GN,1989. Meng SY, Bennett GN,1992. Shi X,1993. Takayama M,1994. Neely MN, Dell CL, Olson ER,1994. Dell CL,1994. Shi X,1995. Reams SG, Lee N, Mat-Jan F, Clark DP,1997. Rowbury RJ,1997. Prüss BM, Markovic D, Matsumura P,1997. Kikuchi Y,1998. Kikuchi Y,1998. Neely MN,1996. Popkin PS, Maas WK,1980. Beretskene SIa, Bruzgulis PA, Ragavichus AB,1980. Watson N,1992.
Based on quantitative analysis, a model was proposed for the Cad system by Fritz et al. Fritz G,2009 The Cad system is conditionally activated by low pH only when a high lysine concentration is available. Lysine inhibits the repressive effects of the lysine permease LysP on the receptor CadC, while low pH activates CadC directly. The active form of CadC activates transcription of the cadBA operon. The Cad system counteracts the elevated H+ concentration by converting lysine to cadaverine under the consumption of H+ and exporting cadaverine in exchange for external lysine. Finally, it is believed that external cadaverine deactivates CadC Fritz G,2009 The cadBA operon displays a transient response, even when the conditions for its induction persist. The Cad system supports negative feedback by external cadaverine as the origin of the transient response Fritz G,2009
LysP indirectly regulates the cadBA operon by sequestering the CadC activator in the absence of Lys, but not in its presence Neely MN, Dell CL, Olson ER,1994. Tetsch L,2008. Marbaniang CN,2011
IHF induces amino acid-dependent acid resistance (AR) by activating cadBA translation at acidic pH Bi H, Zhang C,2014
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Watson N., et al., 1992
Promoter
Name: cadBp
+1: 4360106
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 75
Sequence: tttgtgttatttcacctaatctttaggattaatccttttttcgtgagtaatcttatcgccAgtttggtctggtcaggaaat
                           -35                       -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Watson N., et al., 1992
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor cadBp 4360278 4360292 -179.0 ataatttttaTTACATAAATTTAACcagagaatgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[CadC,+] 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 CadC activator cadBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [4], [9]
[GadE-RcsB,+] 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 GadE-RcsB activator cadBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [8]
[GadX,+] 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 GadX activator cadBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
[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
proximal H-NS repressor cadBp 4360131 4360145 -32.0 tcacctaatcTTTAGGATTAATCCTtttttcgtga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4], [5]
remote H-NS repressor cadBp 4360228 4360242 -129.0 aaacattaaaTGTTTATCTTTTCATgatatcaact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4], [5]
remote H-NS repressor cadBp 4360274 4360288 -175.0 tttttattacATAAATTTAACCAGAgaatgtcacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4], [5]
remote H-NS repressor cadBp 4360359 4360373 -260.0 tgatttatgcTCGGAAATATTTGTTgttgagtttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4], [5]
remote H-NS repressor cadBp 4360416 4360430 -317.0 ccttatgttgTACCTTATCTCGACAaatttcttgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
[Lrp,+] 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 Lrp activator cadBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
[OmpR,-] 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 OmpR repressor cadBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [11]


Transcription unit       
Name: cadA
Gene(s): cadA   Genome Browser M3D Gene expression COLOMBOS
Note(s): During acid stress, RavA antagonizes the inhibitory effect of ppGpp on CadA activity El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA,2010.
The mRNA produced by the cadA gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Fluoroquinolones and -lactams increased cadA expression, while an aminoglycoside (amikacin) decreased such expression Akhova A,.
Promoter
Name: cadAp
+1: Unknown
Evidence: [EXP-IEP]
Reference(s): [12] Zaslaver A., et al., 2006


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-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IMP] Inferred from mutant phenotype

 [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

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Watson N., Dunyak DS., Rosey EL., Slonczewski JL., Olson ER., 1992, Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH., J Bacteriol 174(2):530-40

 [2] 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

 [3] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [4] Kuper C., Jung K., 2005, CadC-mediated activation of the cadBA promoter in Escherichia coli., J Mol Microbiol Biotechnol 10(1):26-39

 [5] Shi X., Waasdorp BC., Bennett GN., 1993, Modulation of acid-induced amino acid decarboxylase gene expression by hns in Escherichia coli., J Bacteriol 175(4):1182-6

 [6] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [7] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [8] Krin E., Danchin A., Soutourina O., 2010, RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli., Res Microbiol 161(5):363-371

 [9] Brameyer S., Rosch TC., El Andari J., Hoyer E., Schwarz J., Graumann PL., Jung K., 2019, DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family., Commun Biol 2:4

 [10] Ruiz J., Haneburger I., Jung K., 2011, Identification of ArgP and Lrp as transcriptional regulators of lysP, the gene encoding the specific lysine permease of Escherichia coli., J Bacteriol 193(10):2536-48

 [11] Chakraborty S., Winardhi RS., Morgan LK., Yan J., Kenney LJ., 2017, Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells., Nat Commun 8(1):1587

 [12] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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