RegulonDB RegulonDB 11.1: Operon Form
   

wza-wzb-wzc-wcaAB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: wza-wzb-wzc-wcaAB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: wzbc
Gene(s): wzc, wzb, wza   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of this operon is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013.
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Rhodius VA., et al., 2005
Promoter
Name: wzap2
+1: 2137193
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: -50
Sequence: taaataaacaatgatgaaatccaaaatgaaattgatgccattattggtgtcagtaaccttGataagcggttgcacagtact
Note(s): The wza gene may have been misannotated, because the transcription start site of wzap2 is 50 bp downstream of the start site of the gene Rhodius VA,2005
Evidence: [COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Rhodius VA., et al., 2005


Transcription unit          
Name: wza-wzb-wzc-wcaAB
Synonym(s): OP00290, cps, cpsB, cpsGB
Gene(s): wcaB, wcaA, wzc, wzb, wza   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [2] Ebel W., et al., 1999
[3] Stout V. 1996
Promoter
Name: wzap1
+1: 2137583
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 340
Sequence: atagccaattaccgaattgttatcttgcctgctattccgttagctgtaacacttcctcctGcattattggaaagccaatat
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[3] Stout V. 1996
TF binding sites (TFBSs)
[RcsAB,+] 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 RcsAB activator wzap1 2137659 2137673 -83.0 taaaaaccatATTGAATGACACTTAatataattct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
remote RcsAB activator wzap1 2137681 2137695 -105.0 attgtcaaccTAAAGAAACTCCTAAaaaccatatt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5], [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.3 2133408 2133437 tcacgccgcaTCCGGCAAGCAAACCAGCTCATAAGCCGGgagaacaacc
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg
Strand: reverse
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  JUMPstart RNA 57.3 2137422 2137460 uaaacuaaauCAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUGucuggaugcc
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [2] Ebel W., Trempy JE., 1999, Escherichia coli RcsA, a positive activator of colanic acid capsular polysaccharide synthesis, functions To activate its own expression., J Bacteriol 181(2):577-84

 [3] Stout V., 1996, Identification of the promoter region for the colanic acid polysaccharide biosynthetic genes in Escherichia coli K-12., J Bacteriol 178(14):4273-80

 [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] Gottesman S., Stout V., 1991, Regulation of capsular polysaccharide synthesis in Escherichia coli K12., Mol Microbiol 5(7):1599-606

 [6] Wehland M., Bernhard F., 2000, The RcsAB box. Characterization of a new operator essential for the regulation of exopolysaccharide biosynthesis in enteric bacteria., J Biol Chem 275(10):7013-20

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