RegulonDB RegulonDB 11.2: Operon Form
   

dinG-ybiB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: dinG-ybiB
Gene(s): dinG, ybiB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP] Inferred from expression pattern
Reference(s): [1] Kaleta C., et al., 2010
[2] Schneider D., et al., 2015
Promoter
Name: dinGp
+1: 833073
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: -3
Sequence: ctgaaaaccgaaaaatgccacaatattggctgtttatacagtatttcaggttttctcatgGcattaaccgccgcgcttaaa
                          -35                  -10          +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the promoters, whose transcription start sites were determined experimentally, present a distance of 6 nucleotides between the transcription start site and the -10 box.
Lewis LK,1992predicted a potential dinG promoter site (-35 and -10 regions) by using three different computational search programs. The putative transcription start site of this promoter overlaps the dinG gene, but the start of the translation of this gene has not been determined.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Huerta AM., et al., 2003
[4] Lewis LK., et al., 1992
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 dinGp 833036 833055 -27.5 aatgccacaaTATTGGCTGTTTATACAGTAtttcaggttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5]


Transcription unit       
Name: ybiB
Gene(s): ybiB   Genome Browser M3D Gene expression COLOMBOS
Note(s): In conjunction with gene expression analysis, it can be argued that the ybiB and dinG genes form an operon regulated by LexA Kaleta C,2010
Based on crystallization analysis and EMSA, it was determined that YbiB binds to DNA with high affinity. The ybiB gene is under LexA control and is induced by DNA-damaging agents Schneider D,2015.
Evidence: [COMP-HINF] Inferred by a human based on computational evidence


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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


Reference(s)    

 [1] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116

 [2] Schneider D., Kaiser W., Stutz C., Holinski A., Mayans O., Babinger P., 2015, YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins., J Biol Chem 290(32):19527-39

 [3] 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

 [4] Lewis LK., Jenkins ME., Mount DW., 1992, Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor., J Bacteriol 174(10):3377-85

 [5] Lewis LK., Mount DW., 1992, Interaction of LexA repressor with the asymmetric dinG operator and complete nucleotide sequence of the gene., J Bacteriol 174(15):5110-6

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