RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: metNIQ
Synonym(s): abc
Gene(s): metQ, metI, metN   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 metQ . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [IEP] Inferred from expression pattern
[ITC] Inferred through co-regulation
Reference(s): [1] Merlin C., et al., 2002
Promoter
Name: metNp
+1: 222714
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: aaagtgctcttcgcataaacctgattgatttagacgtctggatgccttaacatccatttcAttgacggcgttgcccgtttc
                         -35                    -10         +1                   
Evidence: [HIPP]
[ICA]
[RS-EPT-CBR]
Reference(s): [2] Gal J., et al., 2002
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[HypT,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HypT-Met-oxidized activator metNp nd nd nd nd nd [BPP], [GEA] [6], [7]
[MetJ-S-adenosylmethionine,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetJ-S-adenosylmethionine repressor metNp 222724 222739 -17.5 tgatttagacGTCTGGATGCCTTAACatccatttca nd [AIBSCS], [CV(GEA)], [GEA] [2], [4], [5]
proximal MetJ-S-adenosylmethionine repressor metNp 222732 222747 -25.5 aacctgattgATTTAGACGTCTGGATgccttaacat nd [AIBSCS], [APIORCISFBSCS] [1], [2], [4], [5]


Evidence    

 [HIPP] Human inference of promoter position

 [ICA] Inferred by computational analysis

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA)] cross validation(GEA)

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Merlin C., Gardiner G., Durand S., Masters M., 2002, The Escherichia coli metD locus encodes an ABC transporter which includes Abc (MetN), YaeE (MetI), and YaeC (MetQ)., J Bacteriol 184(19):5513-7

 [2] Gal J., Szvetnik A., Schnell R., Kalman M., 2002, The metD D-methionine transporter locus of Escherichia coli is an ABC transporter gene cluster., J Bacteriol 184(17):4930-2

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] 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

 [5] 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

 [6] 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

 [7] 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

RegulonDB