RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: recAX
Gene(s): recX, recA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Pages V., et al., 2003
[2] Stohl EA., et al., 2003
Promoter
Name: recAp
+1: 2823819
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 50
Sequence: cttgtggcaacaatttctacaaaacacttgatactgtatgagcatacagtataattgcttCaacagaacatattgactatc
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[1] Pages V., et al., 2003
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 recAp 2823829 2823848 -20.0 aaacacttgaTACTGTATGAGCATACAGTAtaattgcttc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]


Transcription unit          
Name: recA
Synonym(s): OP00086
Gene(s): recA   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
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for recA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [5] Clark AJ., et al., 1994
[6] Fernandez De Henestrosa AR., et al., 2000
Promoter
Name: recAp
+1: 2823819
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 50
Sequence: cttgtggcaacaatttctacaaaacacttgatactgtatgagcatacagtataattgcttCaacagaacatattgactatc
                                 -35                   -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[1] Pages V., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: aaaagcaaaaGGGCCGCAGATGCGACCCttgtgtatca
Reference(s): [1] Pages V., et al., 2003
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 recAp 2823829 2823848 -20.0 aaacacttgaTACTGTATGAGCATACAGTAtaattgcttc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.0 2822657 2822692 ttgtttgataCACAAGGGTCGCATCTGCGGCCCTTTTGCTTTTTTaagttgtaag
  anti-terminator -10.3 2822678 2822746 ctctgtagatGATAGCGAAGGCGTAGCAGAAACTAACGAAGATTTTTAATCGTCTTGTTTGATACACAAGGGTCGCATctgcggccct
  anti-anti-terminator -9.5 2822733 2822767 cccgaactcaACGCCGGATTTCTCTGTAGATGATAGCGAAGGCGtagcagaaac
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-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

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


Reference(s)    

 [1] Pages V., Koffel-Schwartz N., Fuchs RP., 2003, recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli., DNA Repair (Amst) 2(3):273-84

 [2] Stohl EA., Brockman JP., Burkle KL., Morimatsu K., Kowalczykowski SC., Seifert HS., 2003, Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo., J Biol Chem 278(4):2278-85

 [3] 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

 [4] Little JW., Mount DW., Yanisch-Perron CR., 1981, Purified lexA protein is a repressor of the recA and lexA genes., Proc Natl Acad Sci U S A 78(7):4199-203

 [5] Clark AJ., Sandler SJ., 1994, Homologous genetic recombination: the pieces begin to fall into place., Crit Rev Microbiol 20(2):125-42

 [6] Fernandez De Henestrosa AR., Ogi T., Aoyagi S., Chafin D., Hayes JJ., Ohmori H., Woodgate R., 2000, Identification of additional genes belonging to the LexA regulon in Escherichia coli., Mol Microbiol 35(6):1560-72

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