RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: gyrB
Gene(s): gyrB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for gyrB . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Adachi T., et al., 1984
Promoter
Name: gyrBp
+1: 3880150
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: atagacatgtcggacgaaaattcgaagatgtttaccgtggaaaagggtaaaataacggatTaacccaagtataaatgagcg
                          -35                        -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [1] Adachi T., et al., 1984
[2] Huerta AM., et al., 2003
[3] Maciag A., et al., 2011
[4] Menzel R., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: ataattgcggATTGCAGAAATAAAAAGGGCGGAGATGATCTCCGCCCTTTTCTTATAGCTTCTTGccggatgcgg
Reference(s): [5] Feng CQ., et al., 2019
[6] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor gyrBp 3880205 3880219 -62.0 gatcagtgctGAACACGTTATAGACatgtcggacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [8]
remote Fis repressor gyrBp 3880252 3880266 -109.0 cttgccagccGCTTAAAAGCGACGCaatcacaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [8]


Transcription unit          
Name: gyrB
Gene(s): gyrB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for gyrB . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Adachi T., et al., 1984
Promoter
Name: gyrBp2
+1: 3880150
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 31
Sequence: atagacatgtcggacgaaaattcgaagatgtttaccgtggaaaagggtaaaataacggatTaacccaagtataaatgagcg
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [1] Adachi T., et al., 1984
[2] Huerta AM., et al., 2003
[9] Lelong C., et al., 2007
[3] Maciag A., et al., 2011
[4] Menzel R., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: ataattgcggATTGCAGAAATAAAAAGGGCGGAGATGATCTCCGCCCTTTTCTTATAGCTTCTTGccggatgcgg
Reference(s): [5] Feng CQ., et al., 2019
[6] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor gyrBp2 3880205 3880219 -62.0 gatcagtgctGAACACGTTATAGACatgtcggacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [8]
remote Fis repressor gyrBp2 3880252 3880266 -109.0 cttgccagccGCTTAAAAGCGACGCaatcacaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP] Inferred from mutant phenotype

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

 [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] Inferred from expression pattern


Reference(s)    

 [1] Adachi T., Mizuuchi K., Menzel R., Gellert M., 1984, DNA sequence and transcription of the region upstream of the E. coli gyrB gene., Nucleic Acids Res 12(16):6389-95

 [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] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [4] Menzel R., Gellert M., 1987, Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters., Proc Natl Acad Sci U S A 84(12):4185-9

 [5] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [6] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [7] Cameron AD., Stoebel DM., Dorman CJ., 2011, DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica., Mol Microbiol 80(1):85-101

 [8] Schneider R., Travers A., Kutateladze T., Muskhelishvili G., 1999, A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli., Mol Microbiol 34(5):953-64

 [9] Lelong C., Aguiluz K., Luche S., Kuhn L., Garin J., Rabilloud T., Geiselmann J., 2007, The Crl-RpoS regulon of Escherichia coli., Mol Cell Proteomics 6(4):648-59

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