RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: artJ
Gene(s): artJ   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral Chueca B, Pérez-Sáez E, Pagán R, García-Gonzalo D,2017.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Wissenbach U., et al., 1993
[2] Wissenbach U., et al., 1995
Promoter
Name: artJp
+1: 900626
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: catttaaattatttaatcatgtttattgcatataaattcacttgatggcattgttatcccAtgccgcagacacggccaaaa
                               -35                    -10   +1                   
Note(s): Inhibition of artJp by ArgR is mediated by steric exclusion of the RNA polymerase Caldara M,2007
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Caldara M., et al., 2007
[4] Huerta AM., et al., 2003
[5] Maciag A., et al., 2011
[6] Salgado H, et al., 2012
[2] Wissenbach U., et al., 1995
Terminator(s)
Type: rho-dependent
Sequence: agcaataaaaAAGCCGCATGTGCGGCTTcagattgctg
Reference(s): [2] Wissenbach U., et al., 1995
TF binding sites (TFBSs)
[ArgR,-] 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 ArgR-L-arginine repressor artJp 900645 900663 -27.5 taatcatgttTATTGCATATAAATTCACTtgatggcatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [7]
proximal ArgR-L-arginine repressor artJp 900666 900684 -48.5 ttttatttcaTTTAAATTATTTAATCATGtttattgcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.0 900687 900726 ttcttataatGAAGACGGACAACCCACTAAGTTGTCCGTCTTTTTTATTtcatttaaat
  anti-terminator -5.6 900718 900758 ggacgccttaTCCGGCCTACATAGTGCATAAATTCTTATAATGAAGACGGacaacccact
  anti-anti-terminator -31.5 900742 900795 tcagacatcaGCACGGTGCCTGTGCCGGATGCGGCGGGGACGCCTTATCCGGCCTACATAGTGcataaattct
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] Inferred by a human based on computational evidence

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

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

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

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

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IEP-MICROARRAY] Expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-EXO] ChIP-exo evidence


Reference(s)    

 [1] Wissenbach U., Keck B., Unden G., 1993, Physical map location of the new artPIQMJ genes of Escherichia coli, encoding a periplasmic arginine transport system., J Bacteriol 175(11):3687-8

 [2] Wissenbach U., Six S., Bongaerts J., Ternes D., Steinwachs S., Unden G., 1995, A third periplasmic transport system for L-arginine in Escherichia coli: molecular characterization of the artPIQMJ genes, arginine binding and transport., Mol Microbiol 17(4):675-86

 [3] Caldara M., Minh PN., Bostoen S., Massant J., Charlier D., 2007, ArgR-dependent repression of arginine and histidine transport genes in Escherichia coli K-12., J Mol Biol 373(2):251-67

 [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] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [6] 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.

 [7] Caldara M., Charlier D., Cunin R., 2006, The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation., Microbiology 152(Pt 11):3343-54

RegulonDB