RegulonDB RegulonDB 10.6.3: 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 |CITS: [2527331], [1556086], [8381784], [8022268], [8195083], [7830562], [7836317], [9075621], [9172436], [9171439], [9692215], [9692215], [8808945], [6767681], [7001435], [1370290]|.
Based on quantitative analysis, a model was proposed for the Cad system by Fritz et al. |CITS:[19703467]|. 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 |CITS:[19703467]|. 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 |CITS:[19703467]|.
LysP indirectly regulates the cadBA operon by sequestering the CadC activator in the absence of Lys, but not in its presence |CITS:[8195083][18086202][21890697]|.
IHF induces amino acid-dependent acid resistance (AR) by activating cadBA translation at acidic pH |CITS:[24816374]|.
Evidence: [PM] 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
                      -10                       -35         +1                   
Evidence: [HIPP]
[IMP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] Watson N., et al., 1992
TF binding sites (TFBSs)
[ArcA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-Phosphorylated repressor cadBp 4360278 4360292 -179.0 ataatttttaTTACATAAATTTAACcagagaatgt nd [AIBSCS], [GEA] [6]
[CadC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CadC activator cadBp nd nd nd nd nd [BPP], [GEA] [1], [3]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadE-RcsB activator cadBp nd nd nd nd nd [BPP], [GEA] [7], [8]
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadX activator cadBp nd nd nd nd nd [GEA] [7]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal H-NS1 repressor cadBp 4360131 4360145 -32.0 tcacctaatcTTTAGGATTAATCCTtttttcgtga nd [AIBSCS], [BPP], [GEA] [2], [3], [5]
remote H-NS2 repressor cadBp 4360228 4360242 -129.0 aaacattaaaTGTTTATCTTTTCATgatatcaact nd [AIBSCS], [BPP], [GEA] [2], [3], [5]
remote H-NS3 repressor cadBp 4360274 4360288 -175.0 tttttattacATAAATTTAACCAGAgaatgtcacg nd [AIBSCS], [BPP], [GEA] [2], [3], [5]
remote H-NS4 repressor cadBp 4360359 4360373 -260.0 tgatttatgcTCGGAAATATTTGTTgttgagtttt nd [AIBSCS], [BPP], [GEA] [2], [3], [5]
remote H-NS5 repressor cadBp 4360416 4360430 -317.0 ccttatgttgTACCTTATCTCGACAaatttcttgc nd [AIBSCS], [BPP], [GEA] [2], [3], [4]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp activator cadBp nd nd nd nd nd [BPP], [GEA] [9]
[OmpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd OmpR1 repressor cadBp nd nd nd nd nd [BPP], [GEA] [10]
Note(s): 1Hns repress the cadB promoter at pH 8.0
2Hns repress the cadB promoter at pH 8.0
3Hns repress the cadB promoter at pH 8.0
4Hns repress the cadB promoter at pH 8.0
5Hns repress the cadB promoter at pH 8.01Under acid stress at pH 6.5, OmpR repressed the cadBA operon to eliminate proton consumption and acidify the cytoplasm Chakraborty S,2017
The cadBA operon was the major system that eliminated protons upon acid stress over the approximate pH range of 6.1-6.5 Chakraborty S,2017.
OmpR in its dimeric state binds DNA, but phosphorylation of OmpR is not required Chakraborty S,2017
1Hns repress the cadB promoter at pH 8.0
2Hns repress the cadB promoter at pH 8.0
4Hns repress the cadB promoter at pH 8.0
5Hns repress the cadB promoter at pH 8.0
6Hns repress the cadB promoter at pH 8.0
11Under acid stress at pH 6.5, OmpR repressed the cadBA operon to eliminate proton consumption and acidify the cytoplasm Chakraborty S,2017
The cadBA operon was the major system that eliminated protons upon acid stress over the approximate pH range of 6.1-6.5 Chakraborty S,2017.
OmpR in its dimeric state binds DNA, but phosphorylation of OmpR is not required Chakraborty S,2017


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 |CITS: [21148420]|.
Promoter
Name: cadAp
+1: Unknown
Evidence: [IEP]
Reference(s): [11] Zaslaver A., et al., 2006


Evidence    

 [HIPP] Human inference of promoter position

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [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] 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

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

 [4] Laurent G., Calemard E., Charra B., 1988, Dialysis related amyloidosis., Kidney Int Suppl 24:S32-4

 [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] 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

 [10] 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

 [11] 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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