RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: metBL
Gene(s): metB, metL   Genome Browser M3D Gene expression COLOMBOS
Note(s): It has been observed that the transcriptional regulator IHF binds near the start gene of metL Kasho K,2021.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Greene RC., et al., 1984
Promoter
Name: metBp
+1: 4128636
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 36
Sequence: aagaagtttagatgtccagatgtattgacgtccattaacacaatgtttactctggtgcctGacatttcaccgacaaagccc
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kirby TW., et al., 1986
Terminator(s)
Type: rho-independent
Sequence: agtacatggtTAGTTTATATTTGCAGTCCGGTTTGCTTTGCATACCGGATTTTCTTTTTCTTACCatcctgaagt
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[HypT,+] 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 HypT-Met-oxidized activator metBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9], [10]
[MetJ,-] 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 MetJ-S-adenosyl-L-methionine repressor metBp 4128572 4128587 -56.5 tcaatctataCGCAAAGAAGTTTAGAtgtccagatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
proximal MetJ-S-adenosyl-L-methionine repressor metBp 4128580 4128595 -48.5 tacgcaaagaAGTTTAGATGTCCAGAtgtattgacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
proximal MetJ-S-adenosyl-L-methionine repressor metBp 4128582 4128597 -46.5 cgcaaagaagTTTAGATGTCCAGATGtattgacgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
proximal MetJ-S-adenosyl-L-methionine repressor metBp 4128588 4128603 -40.5 gaagtttagaTGTCCAGATGTATTGAcgtccattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
proximal MetJ-S-adenosyl-L-methionine repressor metBp 4128590 4128605 -38.5 agtttagatgTCCAGATGTATTGACGtccattaaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
proximal MetJ-S-adenosyl-L-methionine repressor metBp 4128598 4128613 -30.5 tgtccagatgTATTGACGTCCATTAAcacaatgttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [6], [7]
[PhoP,+] 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 PhoP-phosphorylated activator metBp 4128608 4128624 -20.0 tattgacgtcCATTAACACAATGTTTActctggtgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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


Reference(s)    

 [1] Greene RC., Smith AA., 1984, Insertion mutagenesis of the metJBLF gene cluster of Escherichia coli K-12: evidence for an metBL operon., J Bacteriol 159(2):767-9

 [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] Kirby TW., Hindenach BR., Greene RC., 1986, Regulation of in vivo transcription of the Escherichia coli K-12 metJBLF gene cluster., J Bacteriol 165(3):671-7

 [4] 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

 [5] 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

 [6] Liu R., Blackwell TW., States DJ., 2001, Conformational model for binding site recognition by the E.coli MetJ transcription factor., Bioinformatics 17(7):622-33

 [7] Marincs F., Manfield IW., Stead JA., McDowall KJ., Stockley PG., 2006, Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor., Biochem J 396(2):227-34

 [8] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [9] Drazic A., Miura H., Peschek J., Le Y., Bach NC., Kriehuber T., Winter J., 2013, Methionine oxidation activates a transcription factor in response to oxidative stress., Proc Natl Acad Sci U S A 110(23):9493-8

 [10] Gebendorfer KM., Drazic A., Le Y., Gundlach J., Bepperling A., Kastenmuller A., Ganzinger KA., Braun N., Franzmann TM., Winter J., 2012, Identification of a Hypochlorite-specific Transcription Factor from Escherichia coli., J Biol Chem 287(9):6892-903

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