RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: argG
Gene(s): argG   Genome Browser M3D Gene expression COLOMBOS
Note(s): It has been suggested that a DNA loop is formed when ArgRbinds to the three Arg boxes. The binding of each of two regulators (CRP and ArgR) to the regulatory region of the argG gene interferes with the binding of each of the regulators, but ArgR binding overrides CRP binding.
CRP binds in just one site, activates argG gene expression, and represses the expression of the divergent operon metY-yhbC-nusA-infB.
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied 28644990. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes 28644990. 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 28644990.
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: argGp
+1: 3318562
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 75
Sequence: tttacaaaaaacacactaaactcttcctgtctccgataaaagatgattaaatgaaaactcAtttattttgcataaaaattc
                           -35                  -10         +1                   
Evidence: [AIPP]
Reference(s): [1] Krin E., et al., 2003
TF binding sites (TFBSs)
[ArgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArgR-L-arginine repressor argGp 3318428 3318445 -125.5 ttgctaatcaTGTGAATGAATATCCAGTtcactttcat nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [2], [3], [4]
proximal ArgR-L-arginine repressor argGp 3318547 3318564 -6.5 ataaaagatgATTAAATGAAAACTCATTtattttgcat nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [2], [3], [4]
proximal ArgR-L-arginine repressor argGp 3318568 3318585 15.5 actcatttatTTTGCATAAAAATTCAGTgagagcggaa nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1], [2], [3], [4]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 activator argGp 3318384 3318405 -167.5 ctgcaggcatTATAGTGATCCACGCCACATTTtgtcaacgtt nd [BPP], [CV(SM)], [GEA], [SM] [1]
Note(s): 1Krin E,2003reported that this site is at -166.5, but when identifying the sequence in the genome, it is centered at -167.5. This site overlaps the putative -10 box of the divergently transcribed upstream metY gene.1Krin E,2003reported that this site is at -166.5, but when identifying the sequence in the genome, it is centered at -167.5. This site overlaps the putative -10 box of the divergently transcribed upstream metY gene.


Evidence    

 [AIPP] Automated inference of promoter position

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis

 [CV(SM)] cross validation(SM)

 [SM] Site mutation


Reference(s)    

 [1] Krin E., Laurent-Winter C., Bertin PN., Danchin A., Kolb A., 2003, Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12., J Bacteriol 185(10):3139-46

 [2] 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

 [3] Charlier D., Roovers M., Van Vliet F., Boyen A., Cunin R., Nakamura Y., Glansdorff N., Pierard A., 1992, Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression., J Mol Biol 226(2):367-86

 [4] Makarova KS., Mironov AA., Gelfand MS., 2001, Conservation of the binding site for the arginine repressor in all bacterial lineages., Genome Biol 2(4):RESEARCH0013

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