RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: paaABCDEFGHIJK
Gene(s): paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK   Genome Browser M3D Gene expression COLOMBOS
Note(s): Some, but not all, E. coli K-12 strains lack the ability to utilize phenylacetate; E. coli strains MG1655 and W exhibit utilization, although E. coli C does not exhibit utilization due to deletion of a large fragment that includes the paa region Ferrandez A,1998.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Ferrandez A., et al., 1998
Promoter
Name: paaAp
+1: 1453865
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 62
Sequence: atccgtcacagttcaaacatacaaaatttgtgattttacttaactattgtgtaactttcaTaaaacaatgtgattcgtgtt
                   -35                       -10            +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Ferrandez A., et al., 1998
[2] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 activator paaAp 1453796 1453817 -58.5 tataaaaataGGGTGCGAAATCCGTCACAGTTCaaacatacaa nd [APIORCISFBSCS], [BPP], [GEA], [SM] [5]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 activator paaAp 1453744 1453756 -115.0 gcgatctgtaTAGCAACTGCGGAAaacattaatg nd [APIORCISFBSCS], [BPP], [GEA], [SM] [5]
[PaaX,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PaaX repressor paaAp 1453875 1453913 30.0 taaaacaatgTGATTCGTGTTTTTAATTAATTCACGAAAACTGGAATCGTaaaggtgatg nd [APIORCISFBSCS], [BCE], [GEA], [SM] [5], [6]
[SlyA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SlyA activator paaAp 1453688 1453687 -177.5 atagttaaatCgcgaatcata nd [AIBSCS], [BPP], [GEA] [3], [4]
proximal SlyA activator paaAp 1453791 1453790 -74.5 tgatttataaAaatagggtgc nd [AIBSCS], [BPP], [GEA] [3], [4]
proximal SlyA activator paaAp 1453846 1453845 -19.5 gattttacttAactattgtgt nd [AIBSCS], [BPP], [GEA] [3], [4]
Note(s): 1This site of CRP binding is also used to regulate the divergent paaZp promoter.1This site of IHF binding is also used to regulate the divergent paaZp promoter.2This site of IHF binding is also used to regulate the divergent paaZp promoter.
4This site of CRP binding is also used to regulate the divergent paaZp promoter.


Transcription unit       
Name: paaJ
Gene(s): paaJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Li Z., et al., 2019
Promoter
Name: paaJp3
+1: 1460644
Distance from start of the gene: 249
Sequence: gaccgtcactgcacaaatgcttaacggtcatcaaagttgccacggcgggcagctattttcActggctgatactgcctttgc
Evidence: [RSE]
[TIM]
Reference(s): [7] Li Z., et al., 2019


Transcription unit       
Name: paaJ
Gene(s): paaJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Li Z., et al., 2019
Promoter
Name: paaJp2
+1: 1460771
Distance from start of the gene: 122
Sequence: acgattgattttttgcgtccaggctttgccggagacaccttaactgctactgcgcaggtaCgtcatcagggcaagcaaacc
Evidence: [RSE]
[TIM]
Reference(s): [7] Li Z., et al., 2019


Transcription unit       
Name: paaJ
Gene(s): paaJ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Li Z., et al., 2019
Promoter
Name: paaJp
+1: 1460801
Distance from start of the gene: 92
Sequence: ggagacaccttaactgctactgcgcaggtacgtcatcagggcaagcaaaccggtgtttacGacatcgaaattgttaaccaa
Evidence: [RSE]
[TIM]
Reference(s): [7] Li Z., et al., 2019


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [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

 [SM] Site mutation

 [BCE] Binding of cellular extracts

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [RSE] RNA-seq evidence


Reference(s)    

 [1] Ferrandez A., Minambres B., Garcia B., Olivera ER., Luengo JM., Garcia JL., Diaz E., 1998, Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway., J Biol Chem 273(40):25974-86

 [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] Bartoli J., Viala JP., Bouveret E., 2020, SlyA Transcriptional Regulator Is Not Directly Affected by ppGpp Levels., Front Microbiol 11:1856

 [4] Curran TD., Abacha F., Hibberd SP., Rolfe MD., Lacey MM., Green J., 2017, Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon., Microbiology 163(3):400-409

 [5] Ferrandez A., Garcia JL., Diaz E., 2000, Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli., J Biol Chem 275(16):12214-22

 [6] Kim HS., Kang TS., Hyun JS., Kang HS., 2004, Regulation of penicillin G acylase gene expression in Escherichia coli by repressor PaaX and the cAMP-cAMP receptor protein complex., J Biol Chem 279(32):33253-62

 [7] Li Z., Pan Q., Xiao Y., Fang X., Shi R., Fu C., Danchin A., You C., 2019, Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation., Microb Biotechnol 12(2):360-376

 [8] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74

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