RegulonDB RegulonDB 11.1: Operon Form
   

yiiS-uspD operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: yiiS-uspD
Gene(s): yiiS, uspD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yiiSp
+1: 4112869
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 98
Sequence: gcaaatgacaatacccggaaaatccttctgaactcttcaccttaagcaatatcaaaaaaaAtggtaatccataagatcatt
                              -35                   -10     +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Rezuchova B., et al., 2003
[3] Rhodius VA., et al., 2005
TF binding sites (TFBSs)
[YdeO,+] 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 YdeO activator yiiSp 4112798 4112831 -55.0 cgggattgttATTTCCACGATGCAAATGACAATACCCGGAAAATccttctgaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation yiiSp nd   [EXP-IEP] [5]
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [5] Gustavsson N., et al., 2002


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

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

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

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


Reference(s)    

 [1] 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

 [2] Rezuchova B., Miticka H., Homerova D., Roberts M., Kormanec J., 2003, New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system., FEMS Microbiol Lett 225(1):1-7

 [3] 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

 [4] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962

 [5] Gustavsson N., Diez A., Nystrom T., 2002, The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage., Mol Microbiol 43(1):107-17

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