RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: uvrD
Synonym(s): OP00099
Gene(s): uvrD   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on the bacteriostatic antibiotic-induced persister model, 37 and 9 genes were found to produce defects in rifampin- and tetracycline-induced persister formation, respectively. Only six mutants were found to overlap in both treatment-induced persister screens: recA, recC, ruvA, uvrD, fis, and acrB. Four of these mutants (recA, recC, ruvA, and uvrD) mapped to the DNA repair pathway, one mutant mapped to a global transcriptional regulator (fis), and one to a gene for an efflux protein (acrB) 29559967 Other genes that mapped to transporters, membrane biogenesis, LPS biosynthesis, flagellum biosynthesis, metabolism (folate and energy), and translation were more specific to rifampin-induced persisters 29559967
Reference(s): [1] Arthur HM., et al., 1983
Promoter
Name: uvrDp1
+1: 3997907
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 76
Sequence: tactgccgcatctggaaatttcccggttggcatctctgacctcgctgatataatcagcaaAtctgtatatatacccagctt
                           -35                   -10        +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Arthur HM., et al., 1987
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gtgtaacgttGCCGGATGCGGTGCTGCGCACCTTATTTggcctaaaaa
Reference(s): [4] Finch PW., et al., 1984
TF binding sites (TFBSs)
[LexA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal LexA repressor uvrDp1 3997907 3997926 11.0 taatcagcaaATCTGTATATATACCCAGCTttttggcgga nd [APIORCISFBSCS] [5]


Transcription unit       
Name: uvrD
Gene(s): uvrD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [2] Arthur HM., et al., 1987
Promoter
Name: uvrDp2
+1: 3997971
Distance from start of the gene: 12
Sequence: gtatatatacccagctttttggcggagggcgttgcgcttctccgcccaacctatttttacGcggcggtgccaatggacgtt
Evidence: [TIM]
Reference(s): [2] Arthur HM., et al., 1987
Terminator(s)
Type: rho-independent
Sequence: gtgtaacgttGCCGGATGCGGTGCTGCGCACCTTATTTggcctaaaaa
Reference(s): [4] Finch PW., et al., 1984


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.09 3997940 3997985 ggcggagggcGTTGCGCTTCTCCGCCCAACCTATTTTTACGCGGCGGTGCCAATGgacgtttctt
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    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [CV(TIM)] cross validation(TIM)

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

 [TIM] Transcription initiation mapping

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


Reference(s)    

 [1] Arthur HM., Eastlake PB., 1983, Transcriptional control of the uvrD gene of Escherichia coli., Gene 25(2-3):309-16

 [2] Arthur HM., Cavanagh DR., Finch PW., Emmerson PT., 1987, Regulation of the Escherichia coli uvrD gene in vivo., J Bacteriol 169(8):3435-40

 [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] Finch PW., Emmerson PT., 1984, The nucleotide sequence of the uvrD gene of E. coli., Nucleic Acids Res 12(14):5789-99

 [5] Easton AM., Kushner SR., 1983, Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation., Nucleic Acids Res 11(24):8625-40

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