RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: xapB
Gene(s): xapB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [1] Li Z., et al., 2019
Promoter
Name: xapBp1
+1: 2524251
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 266
Sequence: tcgtatccggggccgaatttcgagactgcggcggaaattcgcatgatgcaaattattggtGgggatgttgttggtatgtct
                           -35                          -10 +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
Reference(s): [1] Li Z., et al., 2019


Transcription unit       
Name: xapB
Gene(s): xapB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [1] Li Z., et al., 2019
Promoter
Name: xapBp2
+1: 2524303
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 318
Sequence: acaaaaagtggcgaaagaagagggtttccctctgacggagggcgtgttcgtctcgtatccGgggccgaatttcgagactgc
                                                        -10 +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
Reference(s): [1] Li Z., et al., 2019
Terminator(s)
Type: rho-independent
Sequence: tatcataaaaGCAGCTCTGAAGAGCAGAGCCGCgaatcctttt


Transcription unit       
Name: xapB
Gene(s): xapB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [1] Li Z., et al., 2019
Promoter
Name: xapBp3
+1: 2524375
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 390
Sequence: taacgatgatcgttttggagagcgcttcttctcactggcaaatgcctacgatgcggaataCcgcgcactgttacaaaaagt
                                         -24        -12     +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP-RNA-SEQ]
Reference(s): [1] Li Z., et al., 2019
Terminator(s)
Type: rho-independent
Sequence: tatcataaaaGCAGCTCTGAAGAGCAGAGCCGCgaatcctttt


Transcription unit          
Name: xapAB
Gene(s): xapB, xapA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on a genetic switch model, it was determined that the expression level of the xapAB operon among cells is bimodal and that the system seems to be bistable Laxhuber KS, Morrison MJ, Chure G, Belliveau NM, Strandkvist C, Naughton KL, Phillips R,2020
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [2] Maciag A., et al., 2011
[3] Seeger C., et al., 1995
Promoter
Name: xapAp2
+1: 2524910
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 32
Sequence: tattgaatgcgtgagaaaagtgtattggtaagagccgggacaacctcgctataaaaaggcGttagattccaccctacagaa
                              -35                      -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[2] Maciag A., et al., 2011
[3] Seeger C., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: tatcataaaaGCAGCTCTGAAGAGCAGAGCCGCgaatcctttt
TF binding sites (TFBSs)
[XapR,+] 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 XapR-xanthosine activator xapAp2 2524943 2524955 -39.0 aatgcgtgagAAAAGTGTATTGGtaagagccgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [5]
remote XapR-xanthosine activator xapAp2 2525023 2525035 -119.0 ggaattaataTCGCCAATACAGTttttaccgtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [5]


Transcription unit          
Name: xapAB
Gene(s): xapB, xapA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on a genetic switch model, it was determined that the expression level of the xapAB operon among cells is bimodal and that the system seems to be bistable Laxhuber KS, Morrison MJ, Chure G, Belliveau NM, Strandkvist C, Naughton KL, Phillips R,2020
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [2] Maciag A., et al., 2011
[3] Seeger C., et al., 1995
Promoter
Name: xapAp
+1: 2524910
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: tattgaatgcgtgagaaaagtgtattggtaagagccgggacaacctcgctataaaaaggcGttagattccaccctacagaa
                              -35                      -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[2] Maciag A., et al., 2011
[3] Seeger C., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: tatcataaaaGCAGCTCTGAAGAGCAGAGCCGCgaatcctttt
TF binding sites (TFBSs)
[XapR,+] 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 XapR-xanthosine activator xapAp 2524943 2524955 -39.0 aatgcgtgagAAAAGTGTATTGGtaagagccgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [5]
remote XapR-xanthosine activator xapAp 2525023 2525035 -119.0 ggaattaataTCGCCAATACAGTttttaccgtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.8 2524010 2524027 aataagaaacGGCCTCGCGGGTGAGGCcaaatgatgc
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

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

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [EXP-IEP] Inferred from expression pattern

 [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.


Reference(s)    

 [1] 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

 [2] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [3] Seeger C., Poulsen C., Dandanell G., 1995, Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli., J Bacteriol 177(19):5506-16

 [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] Jorgensen C., Dandanell G., 1999, Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR., J Bacteriol 181(14):4397-403

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