RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: glpABC
Synonym(s): OP00037
Gene(s): glpA, glpB, glpC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The glpABC operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The transcript of glpABC is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Cole ST., et al., 1988
[2] Ehrmann M., et al., 1987
[3] Larson TJ., et al., 1992
Promoter
Name: glpABCp
+1: 2352583
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 64
Sequence: aatgttcaaaatgacgcatgaaatcacgtttcactttcgaattatgagcgaatatgcgcgAaatcaaacaattcatgtttt
                             -35                     -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [4] Huerta AM., et al., 2003
[3] Larson TJ., et al., 1992
[5] Yang B., et al., 1997
Terminator(s)
Type: rho-independent
Sequence: ctcctttctgATGCCCGGTAAGCATGTGGTTACCGGGCATttttgcgtac
Reference(s): [1] Cole ST., et al., 1988
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor glpABCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]
[CRP,+] 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 CRP-cyclic-AMP activator glpABCp 2352482 2352503 -90.5 ttcataaattAAATGTGAATTGCCGCACACATtattaaataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [7], [8]
proximal CRP-cyclic-AMP activator glpABCp 2352532 2352553 -40.5 aaatgttcaaAATGACGCATGAAATCACGTTTcactttcgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [7]
proximal CRP-cyclic-AMP activator glpABCp 2352572 2352593 -0.5 aattatgagcGAATATGCGCGAAATCAAACAAttcatgtttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [7]
[FNR,+] 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 FNR activator glpABCp 2352536 2352549 -40.5 gttcaaaatgACGCATGAAATCACgtttcacttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
proximal FNR activator glpABCp 2352576 2352589 -0.5 atgagcgaatATGCGCGAAATCAAacaattcatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [9], [10]
[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
remote Fis activator glpABCp 2352396 2352410 -180.0 gtggcccgtgGTCTTATTTATGATTaacagcctga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
remote Fis activator glpABCp 2352460 2352474 -116.0 ttgccgcgatGTTAAGAAAACATTCataaattaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
proximal Fis activator glpABCp 2352508 2352522 -68.0 acacattattAAATAAGATTTACAAaatgttcaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
proximal Fis activator glpABCp 2352515 2352529 -61.0 attaaataagATTTACAAAATGTTCaaaatgacgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
proximal Fis activator glpABCp 2352557 2352571 -19.0 cacgtttcacTTTCGAATTATGAGCgaatatgcgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
remote Fis activator glpABCp 2352610 2352624 35.0 tttttactatGGCTAAATGGTAAAAaacgaacttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[FlhDC,+] 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 FlhDC activator glpABCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [11]
[GlpR,-] 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 GlpR repressor glpABCp 2352483 2352502 -90.5 tcataaattaAATGTGAATTGCCGCACACAttattaaata nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
proximal GlpR repressor glpABCp 2352523 2352542 -50.5 agatttacaaAATGTTCAAAATGACGCATGaaatcacgtt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
proximal GlpR repressor glpABCp 2352555 2352574 -18.5 atcacgtttcACTTTCGAATTATGAGCGAAtatgcgcgaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
proximal GlpR repressor glpABCp 2352574 2352593 1.5 ttatgagcgaATATGCGCGAAATCAAACAAttcatgtttt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
remote GlpR repressor glpABCp 2352614 2352633 41.5 tactatggctAAATGGTAAAAAACGAACTTcagagggata nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.8 2352600 2352625 caattcatgtTTTTACTATGGCTAAATGGTAAAAAacgaacttca
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [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


Reference(s)    

 [1] Cole ST., Eiglmeier K., Ahmed S., Honore N., Elmes L., Anderson WF., Weiner JH., 1988, Nucleotide sequence and gene-polypeptide relationships of the glpABC operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12., J Bacteriol 170(6):2448-56

 [2] Ehrmann M., Boos W., Ormseth E., Schweizer H., Larson TJ., 1987, Divergent transcription of the sn-glycerol-3-phosphate active transport (glpT) and anaerobic sn-glycerol-3-phosphate dehydrogenase (glpA glpC glpB) genes of Escherichia coli K-12., J Bacteriol 169(2):526-32

 [3] Larson TJ., Cantwell JS., van Loo-Bhattacharya AT., 1992, Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12., J Biol Chem 267(9):6114-21

 [4] 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

 [5] Yang B., Gerhardt SG., Larson TJ., 1997, Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12., Mol Microbiol 24(3):511-21

 [6] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [7] Weissenborn DL., Wittekindt N., Larson TJ., 1992, Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12., J Biol Chem 267(9):6122-31

 [8] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [9] Iuchi S., Cole ST., Lin EC., 1990, Multiple regulatory elements for the glpA operon encoding anaerobic glycerol-3-phosphate dehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in Escherichia coli: further characterization of respiratory control., J Bacteriol 172(1):179-84

 [10] Kuritzkes DR., Zhang XY., Lin EC., 1984, Use of phi(glp-lac) in studies of respiratory regulation of the Escherichia coli anaerobic sn-glycerol-3-phosphate dehydrogenase genes (glpAB)., J Bacteriol 157(2):591-8

 [11] Pruss BM., Liu X., Hendrickson W., Matsumura P., 2001, FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions., FEMS Microbiol Lett 197(1):91-7

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