RegulonDB RegulonDB 11.0: Operon Form

ppdAB-ygdB-ppdC-recC operon and associated TUs in Escherichia coli K-12 genome

Name: ppdAB-ygdB-ppdC-recC
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit       
Name: recC
Gene(s): recC   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a region of dyad symmetry upstream of recC, and this may be a region to control the gene expression.
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) Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y,2018 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 Cui P, Niu H, Shi W, Zhang S, Zhang W, Zhang Y,2018
Name: recCp
+1: 2962507
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 79
Sequence: tgccaactggcaggtcaaccgaatgcagacatcgcaggcgggatgtgtcagcatcagcgtTacgctagtttcacccggggg
                          -35                    -10        +1                   
Evidence: [HIPP]
Reference(s): [1] Finch PW., et al., 1986

Transcription unit          
Name: ppdAB-ygdB-ppdC-recC
Gene(s): recC, ppdC, ygdB, ppdB, ppdA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Name: ppdAp
+1: 2964220
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 43
Sequence: gaaattttgcaacgtcctgcaacggcgtaaatagtccggaagatgcgccgaagaaatagaAactggccctcgtcttttttt
                            -35                -10          +1                   
Note(s): Park et al showed in 2001 that transcription of ppdA is highly dependent on alternative factor σF Park K,2001. The transcription expression level was examined in a fliA-mutant background.
Reference(s): [2] Huerta AM., et al., 2003
[3] Park K., et al., 2001
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FlhDC activator ppdAp nd nd nd nd nd [GEA], [BPP] [3]

RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.1 2964312 2964341 atcctgccagAGCCGACGCCAGTGTGCGTCGGTTTTTTTaccctccgtt
  anti-terminator -11.3 2964333 2964378 gggcattaaaGCGCCGGTGGCTATCTAATTACGAAACATCCTGCCAGAGCCGACGccagtgtgcg
  anti-anti-terminator -10.5 2964368 2964394 gctacgatccGCATCCGGGCATTAAAGCGCCGGTGGctatctaatt
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"