RegulonDB RegulonDB 11.1: Operon Form
   

rirA-waaQGPSBOJYZU operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: rfaYZ
Gene(s): waaZ, waaY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The Rho protein appears to negatively regulate expression of the operon waaYZ Hafeezunnisa M, Sen R,2020. Rho loading sites (rut sites) were identified upstream of each gene of the operon Hafeezunnisa M, Sen R,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Lee JH., et al., 2009
Promoter
Name: waaYp
+1: 3801136
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 171
Sequence: aactaaaccgtggcacaaatgggcaatttatccatcggtaaaatactataaaatagctttAgaaaattccccctggaaaga
                         -35                        -10     +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[1] Lee JH., et al., 2009
TF binding sites (TFBSs)
[MarA,+] 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 MarA activator waaYp 3801169 3801188 -43.0 gcaactaaacCGTGGCACAAATGGGCAATTtatccatcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
[SoxS,+] 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 SoxS activator waaYp 3801169 3801188 -42.5 gcaactaaacCGTGGCACAAATGGGCAATTtatccatcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]


Transcription unit       
Name: rfaQGPSBIJYZ-waaU
Synonym(s): rfaQGPSBIJYZK
Gene(s): waaU, waaZ, waaY, waaJ, waaO, waaB, waaS, waaP, waaG, waaQ   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Klena JD., et al., 1992
[4] Klena JD., et al., 1992
[5] Parker CT., et al., 1992
Promoter
Name: waaQp
+1: 3808180
Distance from start of the gene: 82
Sequence: cgtcaaagtaagtgcgttatcagtattcaggtagctgttgagcctggggcggtagcgtgcTtttttctgcttaacttaacc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Clementz T. 1992


Transcription unit       
Name: rirA-rfaQGPSBIJYZ-waaU
Synonym(s): rfaQGPSBIJYZ-waaU, rfaQGPSBIJYZK
Gene(s): waaU, waaZ, waaY, waaJ, waaO, waaB, waaS, waaP, waaG, waaQ, rirA   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Klena JD., et al., 1992
[4] Klena JD., et al., 1992
[5] Parker CT., et al., 1992
Promoter
Name: rirAp
+1: 3808238
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: attttgtgtataaaaatcattcgggtcggattgctgcgaaagaaatgatacactagcacgTcaaagtaagtgcgttatcag
                              -35                     -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Clementz T. 1992
[2] Huerta AM., et al., 2003
[7] Maciag A., et al., 2011


Transcription unit       
Name: rfaZ-waaU
Gene(s): waaU, waaZ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Promoter
Name: waaZp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [EXP-IEP]
Reference(s): [8] Zaslaver A., et al., 2006


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Lee JH., Lee KL., Yeo WS., Park SJ., Roe JH., 2009, SoxRS-mediated lipopolysaccharide modification enhances resistance against multiple drugs in Escherichia coli., J Bacteriol 191(13):4441-50

 [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] Klena JD., Ashford RS., Schnaitman CA., 1992, Role of Escherichia coli K-12 rfa genes and the rfp gene of Shigella dysenteriae 1 in generation of lipopolysaccharide core heterogeneity and attachment of O antigen., J Bacteriol 174(22):7297-307

 [4] Klena JD., Pradel E., Schnaitman CA., 1992, Comparison of lipopolysaccharide biosynthesis genes rfaK, rfaL, rfaY, and rfaZ of Escherichia coli K-12 and Salmonella typhimurium., J Bacteriol 174(14):4746-52

 [5] Parker CT., Kloser AW., Schnaitman CA., Stein MA., Gottesman S., Gibson BW., 1992, Role of the rfaG and rfaP genes in determining the lipopolysaccharide core structure and cell surface properties of Escherichia coli K-12., J Bacteriol 174(8):2525-38

 [6] Clementz T., 1992, The gene coding for 3-deoxy-manno-octulosonic acid transferase and the rfaQ gene are transcribed from divergently arranged promoters in Escherichia coli., J Bacteriol 174(23):7750-6

 [7] 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

 [8] 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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