RegulonDB RegulonDB 11.1: Operon Form
   

dinB-yafNOP operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: dinB-yafNOP
Gene(s): dinB, yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] McKenzie GJ., et al., 2003
Promoter
Name: dinBp
+1: 250880
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 18
Sequence: cgcgttaaatgctgaatctttacgcatttctcaaaccctgaaatcactgtatactttaccAgtgttgagaggtgagcaatg
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Layton JC., et al., 2003
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor dinBp 250864 250883 -6.5 accctgaaatCACTGTATACTTTACCAGTGttgagaggtg nd [COMP-AINF], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [4], [5]


Transcription unit          
Name: dinB-yafNOP
Gene(s): dinB, yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] McKenzie GJ., et al., 2003
Promoter
Name: dinBp2
+1: 250880
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 18
Sequence: cgcgttaaatgctgaatctttacgcatttctcaaaccctgaaatcactgtatactttaccAgtgttgagaggtgagcaatg
                            -35              -10            +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Layton JC., et al., 2003
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor dinBp2 250864 250883 -6.5 accctgaaatCACTGTATACTTTACCAGTGttgagaggtg nd [COMP-AINF], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [4], [5]


Transcription unit          
Name: yafNOP
Gene(s): yafN, yafO, yafP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yafNp
+1: 251969
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: ttgcttgacccgcaaatggaaagacaactggtgctgggattatgatgtatactattatgtAtattctggtgtgcattatta
                               -35                   -10    +1                   
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.
There are two transcription start sites (TSSs) for the yafN promoter. Here we associated the TTS more upstream to this promoter. In addition, Christensen-Dalsgaard et al. (2009) showed -10 and -35 boxes which are far from the normal position Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, Jacq A, Bouloc P,2009 However, the -10 box associated with the yafN promoter also shows an unusual distance Christensen-Dalsgaard M,2010
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [6] Christensen-Dalsgaard M., et al., 2010
[2] Huerta AM., et al., 2003
[7] Zaslaver A., et al., 2006
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor yafNp 251958 251977 -1.5 ttatgatgtaTACTATTATGTATATTCTGGtgtgcattat nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IEP] Inferred from expression pattern

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

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


Reference(s)    

 [1] McKenzie GJ., Magner DB., Lee PL., Rosenberg SM., 2003, The dinB operon and spontaneous mutation in Escherichia coli., J Bacteriol 185(13):3972-7

 [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] Layton JC., Foster PL., 2003, Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli., Mol Microbiol 50(2):549-61

 [4] Gillor O., Vriezen JA., Riley MA., 2008, The role of SOS boxes in enteric bacteriocin regulation., Microbiology 154(Pt 6):1783-92

 [5] Ohmori H., Hatada E., Qiao Y., Tsuji M., Fukuda R., 1995, dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues., Mutat Res 347(1):1-7

 [6] Christensen-Dalsgaard M., Jorgensen MG., Gerdes K., 2010, Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses., Mol Microbiol 75(2):333-48

 [7] 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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