RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: glyA
Synonym(s): OP00267
Gene(s): glyA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Lorenz et al. in 1996 showed that MetR at low concentrations represses the glyA gene, when it binds on the binding site located at -142 Lorenz E,1996, and simultaneously activates the transcription of the hmp gene Membrillo-Hernandez J,1998. In addition, MetR functions as an activator when it binds as a dimer of dimers to binding sites located at -121 and -143 relative to the transcription start site of glyA.
Based on gene expression analysis, it was shown that CsgD could positively regulate glyA expression Herrington MB,2013
Reference(s): [1] Lorenz E., et al., 1995
[2] Steiert JG., et al., 1992
Promoter
Name: glyAp
+1: 2685574
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 67
Sequence: cgtttgcgtaaattcctttgtcaagacctgttatcgcacaatgattcggttatactgttcGccgttgtccaacaggaccgc
                                 -35                    -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Plamann MD., et al., 1983
Terminator(s)
Type: rho-independent
Sequence: taacgtagaaAGGCTTCCCGAAGGAAGCCttgatgatca
Reference(s): [5] Plamann MD., et al., 1983
TF binding sites (TFBSs)
[MetR,+] 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 MetR-L-homocysteine activator glyAp 2685688 2685702 -121.0 catcacaaacCTGAAAAGAAATCCGtttccggttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [6], [7], [8]
remote MetR-L-homocysteine activator glyAp 2685710 2685724 -143.0 atgtgatgaaGTGAAAAATTTGCATcacaaacctg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [6], [7], [8], [9]
[MetR,-] 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 MetR-L-homocysteine repressor glyAp 2685710 2685724 -143.0 atgtgatgaaGTGAAAAATTTGCATcacaaacctg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [6], [7], [8], [9]
[PurR,-] 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 PurR-hypoxanthine repressor glyAp 2685626 2685641 -59.5 cgtagcctgaAGGTAATCGTTTGCGTaaattccttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [6], [10]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

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

 [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-IMP-SITE-MUTATION] Site mutation

 [EXP-IMP] Inferred from mutant phenotype

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


Reference(s)    

 [1] Lorenz E., Stauffer GV., 1995, Characterization of the MetR binding sites for the glyA gene of Escherichia coli., J Bacteriol 177(14):4113-20

 [2] Steiert JG., Kubu C., Stauffer GV., 1992, The PurR binding site in the glyA promoter region of Escherichia coli., FEMS Microbiol Lett 78(2-3):299-304

 [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] Plamann MD., Stauffer GV., 1983, Characterization of the Escherichia coli gene for serine hydroxymethyltransferase., Gene 22(1):9-18

 [5] Plamann MD., Stauffer LT., Urbanowski ML., Stauffer GV., 1983, Complete nucleotide sequence of the E. coli glyA gene., Nucleic Acids Res 11(7):2065-75

 [6] Lorenz E., Stauffer GV., 1996, RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli., Microbiology 142 ( Pt 7):1819-24

 [7] Lorenz E., Stauffer GV., 1996, MetR-mediated repression of the glyA gene in Escherichia coli., FEMS Microbiol Lett 144(2-3):229-33

 [8] Lorenz E., Stauffer GV., 1996, Cooperative MetR binding in the Escherichia coli glyA control region., FEMS Microbiol Lett 137(2-3):147-52

 [9] Membrillo-Hernandez J., Coopamah MD., Channa A., Hughes MN., Poole RK., 1998, A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohaemoglobin) gene by the 'NO releaser', S-nitrosoglutathione: nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region., Mol Microbiol 29(4):1101-12

 [10] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

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