RegulonDB RegulonDB 11.1: Operon Form
   

ycjXF-tyrR operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ycjXF-tyrR
Gene(s): ycjX, ycjF, tyrR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Nonaka G., et al., 2006
Promoter
Name: ycjXp
+1: 1384069
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 48
Sequence: tcgccggtcgatgacaacacgggcagttgataatcaatggcctggcccccacattcatatCcttacgaatgattttttttc
                           -35                 -10          +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Nonaka G., et al., 2006
[3] Wade JT., et al., 2006
TF binding sites (TFBSs)
[PgrR,-] 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
nd PgrR repressor ycjXp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IGI], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Transcription unit          
Name: tyrR
Synonym(s): OP00096
Gene(s): tyrR   Genome Browser M3D Gene expression COLOMBOS
Note(s): In the regulatory region of the tyrR gene there are two TyrR boxes Cornish EC,1986. Pittard AJ,1991 where the protein appears to bind without a cofactor to autorepress the expression of the gene Camakaris H,1982.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [5] Cornish EC., et al., 1986
Promoter
Name: tyrRp
+1: 1386692
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tgtcaatgattgttgacagaaaccttcctgctatccaaatagtgtcatatcatcatattaAttgttcttttttcaggtgaa
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Cornish EC., et al., 1986
[2] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: agtaagcgcgAATATGCCTGATGGTGCAACACCATCAGGCATATTaaattatgct
Reference(s): [5] Cornish EC., et al., 1986
TF binding sites (TFBSs)
[PgrR,-] 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
nd PgrR repressor tyrRp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IGI], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
[TyrR,-] 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
remote TyrR repressor tyrRp 1386588 1386605 -95.5 tatcgggtgcTGACCGGATATCTTTACGccgaagtgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6], [7]
proximal TyrR repressor tyrRp 1386632 1386649 -51.5 tccgtctttgTGTCAATGATTGTTGACAgaaaccttcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [6]


Transcription unit       
Name: ycjXF
Gene(s): ycjX, ycjF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


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] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

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

 [EXP-IGI] Inferred from genetic interaction

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

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

 [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] Nonaka G., Blankschien M., Herman C., Gross CA., Rhodius VA., 2006, Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress., Genes Dev 20(13):1776-89

 [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] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [4] Choi U., Park YH., Kim YR., Seok YJ., Lee CR., 2016, Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli., FEMS Microbiol Lett 363(14)

 [5] Cornish EC., Argyropoulos VP., Pittard J., Davidson BE., 1986, Structure of the Escherichia coli K12 regulatory gene tyrR. Nucleotide sequence and sites of initiation of transcription and translation., J Biol Chem 261(1):403-10

 [6] Camakaris H., Pittard J., 1982, Autoregulation of the tyrR gene., J Bacteriol 150(1):70-5

 [7] Pittard AJ., Davidson BE., 1991, TyrR protein of Escherichia coli and its role as repressor and activator., Mol Microbiol 5(7):1585-92

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