RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: yjjZ
Gene(s): yjjZ   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: yjjZp
+1: 4605777
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: cccgatagcaagggatttatctggcttgcaaatgataaaaattatcatatgatattggttAtcattatcaatgaaagagat
                          -35                   -10         +1                   
Note(s): The yjjZp promoter is significantly affected by ectopic production of a nanoRNase during stationary-phase growth Vvedenskaya IO,2012
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Vassinova N., et al., 2000
[2] Vvedenskaya IO., et al., 2012
TF binding sites (TFBSs)
[Fur,-] 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 Fur-Fe2+ repressor yjjZp 4605741 4605759 -27.0 atttatctggCTTGCAAATGATAAAAATTatcatatgat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [5], [6], [7], [8]
proximal Fur-Fe2+ repressor yjjZp 4605770 4605788 3.0 atcatatgatATTGGTTATCATTATCAATgaaagagatg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [5], [6], [7], [8]
[OxyR,+] 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 OxyR activator yjjZp 4605707 4605723 -62.0 taatcatagcGATAGGTTTACCCGATAgcaagggatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] C [3], [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IEP-RNA-SEQ] RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion


Reference(s)    

 [1] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [2] Vvedenskaya IO., Sharp JS., Goldman SR., Kanabar PN., Livny J., Dove SL., Nickels BE., 2012, Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs., Genes Dev 26(13):1498-507

 [3] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [4] Zheng M., Wang X., Doan B., Lewis KA., Schneider TD., Storz G., 2001, Computation-directed identification of OxyR DNA binding sites in Escherichia coli., J Bacteriol 183(15):4571-9

 [5] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [6] D'Autreaux B., Touati D., Bersch B., Latour JM., Michaud-Soret I., 2002, Direct inhibition by nitric oxide of the transcriptional ferric uptake regulation protein via nitrosylation of the iron., Proc Natl Acad Sci U S A 99(26):16619-24

 [7] Gerken H., Vuong P., Soparkar K., Misra R., 2020, Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli., mBio 11(3)

 [8] Zhang F., Li B., Dong H., Chen M., Yao S., Li J., Zhang H., Liu X., Wang H., Song N., Zhang K., Du N., Xu S., Gu L., 2020, YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner., Nucleic Acids Res 48(17):9571-9588

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