RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ruvAB
Gene(s): ruvB, ruvA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Benson FE., et al., 1988
[2] Iwasaki H., et al., 1989
[3] Shinagawa H., et al., 1988
Promoter
Name: ruvAp2
+1: 1946016
Distance from start of the gene: 40
Sequence: tcgagacacctcgcaagttttcttcatccttcgctggatatctatccagcatttttttatCatacagcattatctttgatt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Shinagawa H., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: ctctggtagtCCTGGTAAGACGCGAACAGCGTCGCATCAGGcatattgcca
Reference(s): [3] Shinagawa H., et al., 1988
Type: rho-independent
Sequence: gaacacatttGTCGGATGCGGCGCGAGCGCCTTATCCGACctacggttcg
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor ruvAp2 1946026 1946045 -19.5 cttcatccttCGCTGGATATCTATCCAGCAtttttttatc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal LexA repressor ruvAp2 1946079 1946098 -72.5 gaataaattaTACTGTGCCATTTTTCAGTTcatcgagaca nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd nd


Transcription unit          
Name: ruvAB
Gene(s): ruvB, ruvA   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) 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
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Benson FE., et al., 1988
[2] Iwasaki H., et al., 1989
[3] Shinagawa H., et al., 1988
Promoter
Name: ruvAp1
+1: 1946024
Distance from start of the gene: 48
Sequence: tcagttcatcgagacacctcgcaagttttcttcatccttcgctggatatctatccagcatTtttttatcatacagcattat
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Shinagawa H., et al., 1988
Terminator(s)
Type: rho-independent
Sequence: ctctggtagtCCTGGTAAGACGCGAACAGCGTCGCATCAGGcatattgcca
Reference(s): [3] Shinagawa H., et al., 1988
Type: rho-independent
Sequence: gaacacatttGTCGGATGCGGCGCGAGCGCCTTATCCGACctacggttcg
TF binding sites (TFBSs)
[LexA,-] 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 LexA repressor ruvAp1 1946027 1946046 -12.5 tcttcatcctTCGCTGGATATCTATCCAGCatttttttat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal LexA repressor ruvAp1 1946078 1946097 -63.5 aataaattatACTGTGCCATTTTTCAGTTCatcgagacac nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd nd


Evidence    

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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


Reference(s)    

 [1] Benson FE., Illing GT., Sharples GJ., Lloyd RG., 1988, Nucleotide sequencing of the ruv region of Escherichia coli K-12 reveals a LexA regulated operon encoding two genes., Nucleic Acids Res 16(4):1541-9

 [2] Iwasaki H., Shiba T., Nakata A., Shinagawa H., 1989, Involvement in DNA repair of the ruvA gene of Escherichia coli., Mol Gen Genet 219(1-2):328-31

 [3] Shinagawa H., Makino K., Amemura M., Kimura S., Iwasaki H., Nakata A., 1988, Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination., J Bacteriol 170(9):4322-9

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