RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit       
Name: modABC
Gene(s): modA, modB, modC   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: modAp1
+1: 794995
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 94
Sequence: ccgcttagtcgggcattttctttttctcaacttcctgcttttcctgccgatattttttctTatctacctcacaaaggttag
                           -35                -10           +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28 (σF) promoters: TAAAGTTT in the ?35 box and GCCGATAA in the -10 box Yu HH,2006. Therefore, we assigned a putative transcription start site for this promoter based on the observation that the majority of the σ28 promoters, determined experimentally, present an important -10 motif (5'-CGA-3') at the positions -12 to -10 and a distance of 6 nucleotides between the transcription start site and the -10 box Yu HH, Di Russo EG, Rounds MA, Tan M,2006. Yu HH,2006. Park K,2001.
Yu et al. showed in 2006 that transcription of modA is highly dependent on alternative factor σF and can be transcribed by RNA polymerase σ28 in vitro Yu HH,2006.
Evidence: [AIBSCS]
[AIPP]
[HIPP]
[ICWHO]
[IEP]
[IHBCE]
Reference(s): [1] Huerta AM., et al., 2003
[2] Yu HH., et al., 2006
[3] Zhao K., et al., 2007


Transcription unit          
Name: modABC
Gene(s): modA, modB, modC   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [4] Grunden AM., et al., 1996
[5] McNicholas PM., et al., 1997
[6] Rech S., et al., 1996
Promoter
Name: modAp2
+1: 795062
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: ctcacaaaggttagcaataactgctgggaaaattccgagttagtcgttatattgtcgcctAcataacgttacattaagggg
                     -35                        -10         +1                   
Evidence: [HIPP]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[7] Rech S., et al., 1995
[8] Salgado H, et al., 2012
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator modAp2 794989 795010 -62.5 tgccgatattTTTTCTTATCTACCTCACAAAGgttagcaata nd [GEA], [AIBSCS] [9]
[ModE,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ModE-molybdate repressor modAp2 795046 795069 -4.5 ccgagttagtCGTTATATTGTCGCCTACATAACGttacattaag nd [GEA], [BPP], [SM] [10]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [11] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.4 794929 794961 tgattccctgAATGCCCGCTTAGTCGGGCATTTTCTTTTTCTcaacttcctg
  anti-terminator -17.42 794866 794934 cttggtgaagTATTCAACATCTTTTCTGGTGTTGGTAAAAAAGACCAGCCCGGACAAAATCATTGATTCCCTGAATGCccgcttagtc
  anti-anti-terminator -7.8 794870 794891 gtgaagtattCAACATCTTTTCTGGTGTTGGtaaaaaagac
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    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IEP] Inferred from expression pattern

 [IHBCE] Inferred by a human based on computational evidence

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

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [SM] Site mutation


Reference(s)    

 [1] 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

 [2] Yu HH., Kibler D., Tan M., 2006, In Silico Prediction and Functional Validation of {sigma}28-Regulated Genes in Chlamydia and Escherichia coli., J Bacteriol 188(23):8206-8212

 [3] Zhao K., Liu M., Burgess RR., 2007, Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli., Nucleic Acids Res 35(13):4441-52

 [4] Grunden AM., Ray RM., Rosentel JK., Healy FG., Shanmugam KT., 1996, Repression of the Escherichia coli modABCD (molybdate transport) operon by ModE., J Bacteriol 178(3):735-44

 [5] McNicholas PM., Rech SA., Gunsalus RP., 1997, Characterization of the ModE DNA-binding sites in the control regions of modABCD and moaABCDE of Escherichia coli., Mol Microbiol 23(3):515-24

 [6] Rech S., Wolin C., Gunsalus RP., 1996, Properties of the periplasmic ModA molybdate-binding protein of Escherichia coli., J Biol Chem 271(5):2557-62

 [7] Rech S., Deppenmeier U., Gunsalus RP., 1995, Regulation of the molybdate transport operon, modABCD, of Escherichia coli in response to molybdate availability., J Bacteriol 177(4):1023-9

 [8] 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.

 [9] 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

 [10] Grunden AM., Self WT., Villain M., Blalock JE., Shanmugam KT., 1999, An analysis of the binding of repressor protein ModE to modABCD (molybdate transport) operator/promoter DNA of Escherichia coli., J Biol Chem 274(34):24308-15

 [11] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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