RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ugpBAECQ
Gene(s): ugpQ, ugpC, ugpE, ugpA, ugpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ugpBAECQ genes are contiguous and their products are functionally related.
The expression of the gene ugpB is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression appears to be caused by the transcription factor PhoB Marzan LW,2013

A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ugpQ. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
It was determined by Genomic SELEX screening that the upstream region of the gene ugpB is a target of the transcriptional factor CusR Shimada T,2021.
Evidence: [IC] Inferred by curator
Reference(s): [1] Overduin P., et al., 1988
Promoter
Name: ugpBp1
+1: 3592378
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 53
Sequence: tatcttacaaatgtaacaaaaaagttatttttctgtaattcgagcatgtcatgttaccccGcgagcataaaacgcgtgaat
                                  -35                  -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kasahara M., et al., 1991
TF binding sites (TFBSs)
[PhoB,+] 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 PhoB-phosphorylated activator ugpBp1 3592399 3592417 -30.0 tgtaacaaaaAAGTTATTTTTCTGTAATTcgagcatgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
proximal PhoB-phosphorylated activator ugpBp1 3592421 3592439 -52.0 tgacaccttaCTATCTTACAAATGTAACAaaaaagttat nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [4]


Transcription unit          
Name: ugpBAECQ
Gene(s): ugpQ, ugpC, ugpE, ugpA, ugpB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ugpBAECQ genes are contiguous and their products are functionally related.

A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ugpQ. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
It was determined by Genomic SELEX screening that the upstream region of the gene ugpB is a target of the transcriptional factor CusR Shimada T,2021.
Evidence: [IC] Inferred by curator
Reference(s): [1] Overduin P., et al., 1988
Promoter
Name: ugpBp2
+1: 3592426
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 101
Sequence: ttccctcacccacgccgtcaccgccttgtcatctttctgacaccttactatcttacaaatGtaacaaaaaagttatttttc
                              -35                  -10      +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kasahara M., et al., 1991
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ugpBp2 3592442 3592463 -26.5 gccgtcaccgCCTTGTCATCTTTCTGACACCTtactatctta nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd nd
[PhoB,-] 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 PhoB-phosphorylated repressor ugpBp2 3592421 3592439 -4.0 tgacaccttaCTATCTTACAAATGTAACAaaaaagttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
proximal PhoB-phosphorylated repressor ugpBp2 3592443 3592461 -26.0 cgtcaccgccTTGTCATCTTTCTGACACCttactatctt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.7 3590933 3590957 tcgcgtgtagGCCGGATAAGCGAAGCGCATCCGGcacagttcag
  terminator -6.2 3592352 3592365 agcataaaacGCGTGAATTCGCGcattcggtac
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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


Reference(s)    

 [1] Overduin P., Boos W., Tommassen J., 1988, Nucleotide sequence of the ugp genes of Escherichia coli K-12: homology to the maltose system., Mol Microbiol 2(6):767-75

 [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] Kasahara M., Makino K., Amemura M., Nakata A., Shinagawa H., 1991, Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters., J Bacteriol 173(2):549-58

 [4] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

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