RegulonDB RegulonDB 10.9: Operon Form
   

relA-mazEFG operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: mazEFG
Synonym(s): chpRA
Gene(s): mazG, mazF, mazE   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on deletion of rpoS, it has been shown that the stationary-phase sigma factor σs is responsible for resistance to chpRA-mazG-mediated cell death during the stationary growth phase 19251848
Evidence: [ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Aizenman E., et al., 1996
[2] Gross M., et al., 2006
[3] Marianovsky I., et al., 2001
[4] Masuda Y., et al., 1993
[5] Metzger S., et al., 1988
Promoter
Name: mazEp2
+1: 2911355
Distance from start of the gene: 16
Sequence: ccgaaatttgctcgtatctacaatgtagattgatatatactgtatctacatatgatagcgGtttgaggaaagggttatgat
Evidence: [TIM]
Reference(s): [1] Aizenman E., et al., 1996
[3] Marianovsky I., et al., 2001
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator mazEp2 2911401 2911415 -53.5 cgggagttagGCCGAAATTTGCTCGTatctacaatg nd [BPP], [GEA], [SM] [3]
[MazE,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MazE repressor mazEp2 2911363 2911388 -20.0 ctacaatgtaGATTGATATATACTGTATCTACATATgatagcggtt nd [BCE], [GEA], [SM] [3]
proximal MazE repressor mazEp2 2911376 2911403 -34.0 gaaatttgctCGTATCTACAATGTAGATTGATATATACtgtatctaca nd [BCE], [GEA], [SM] [3]
[MazEF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MazE-MazF repressor mazEp2 2911362 2911389 -20.0 tctacaatgtAGATTGATATATACTGTATCTACATATGatagcggttt nd [BCE], [GEA], [SM] [3]
proximal MazE-MazF repressor mazEp2 2911376 2911403 -34.0 gaaatttgctCGTATCTACAATGTAGATTGATATATACtgtatctaca nd [BCE], [GEA], [SM] [3]


Transcription unit          
Name: mazEFG
Synonym(s): chpRA
Gene(s): mazG, mazF, mazE   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on deletion of rpoS, it has been shown that the stationary-phase sigma factor σs is responsible for resistance to chpRA-mazG-mediated cell death during the stationary growth phase 19251848
Evidence: [ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Aizenman E., et al., 1996
[2] Gross M., et al., 2006
[3] Marianovsky I., et al., 2001
[4] Masuda Y., et al., 1993
[5] Metzger S., et al., 1988
Promoter
Name: mazEp1
+1: 2911368
Distance from start of the gene: 29
Sequence: cacgggagttaggccgaaatttgctcgtatctacaatgtagattgatatatactgtatctAcatatgatagcggtttgagg
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Aizenman E., et al., 1996
[3] Marianovsky I., et al., 2001
[6] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator mazEp1 2911401 2911415 -40.5 cgggagttagGCCGAAATTTGCTCGTatctacaatg nd [BPP], [GEA], [SM] [3]
[MazE,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MazE repressor mazEp1 2911363 2911388 -7.0 ctacaatgtaGATTGATATATACTGTATCTACATATgatagcggtt nd [BCE], [GEA], [SM], [BCE], [GEA], [SM] [3]
proximal MazE repressor mazEp1 2911376 2911403 -21.0 gaaatttgctCGTATCTACAATGTAGATTGATATATACtgtatctaca nd [BCE], [GEA], [SM], [BCE], [GEA], [SM] [3]
[MazEF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MazE-MazF repressor mazEp1 2911362 2911389 -7.0 tctacaatgtAGATTGATATATACTGTATCTACATATGatagcggttt nd [BCE], [GEA], [SM], [BCE], [GEA], [SM] [3]
proximal MazE-MazF repressor mazEp1 2911376 2911403 -21.0 gaaatttgctCGTATCTACAATGTAGATTGATATATACtgtatctaca nd [BCE], [GEA], [SM], [BCE], [GEA], [SM] [3]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp inhibition mazEp1 nd   [GEA] [1]
[2]
Evidence: [GEA] Gene expression analysis
Reference(s): [1] Aizenman E., et al., 1996
[2] Gross M., et al., 2006


Transcription unit       
Name: relA
Gene(s): relA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Brown DR., et al., 2014
Promoter
Name: relAp3
+1: 2913700
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 49
Sequence: tggatatgttcccacacacgggacatctggaatcgatggtacttttctcgcgcgttaaatAgttgcgatttgccgatttcg
Evidence: [TIM]
Reference(s): [7] Brown DR., et al., 2014


Transcription unit          
Name: relA-mazEF
Synonym(s): chpA, relA-chpRA
Gene(s): mazF, mazE, relA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on microarray analysis, Traxler et al. (2008) determined that relA positively regulates its own expression Traxler MF,2008
The control exercised by relA, on glycogen levels may result from an interplay of its (p)ppGpp-mediated positive effect on glgCAP transcription, deviation of surplus ATP flux from nucleic acid and protein biosynthetic pathways to glycogen production, and its negative effect on intracellular levels of the GlgC negative effector AMP 19702577
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [4] Masuda Y., et al., 1993
[5] Metzger S., et al., 1988
Promoter
Name: relAp1
+1: 2913829
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 178
Sequence: gtgttatgcagcaaattataaaactggaacctattcgtatagtttatgtatcctgtaaccCtgcaacgctggctcgggata
                        -35                      -10        +1                   
Note(s): The RelA production is controlled by two promoters, relAp1 and relAp2. relAp1 is a constitutive promoter, which is mainly responsible for RelA production during log phase. relAp2, which is fine-tuned by the global regulators CRP, H-NS, and RpoS, is induced temporarily at the transition state between the exponential growth and stationary phases. Both promoters are required for maximal accumulation of RelA during stationary phase. There is a UP element-like sequence immediately after the -35 box of the relAp1 promoter which is essential for promoter activity (based on a mutation of the putative UP element) Nakagawa A,2006.
Evidence: [HTTIM]
[ICWHO]
[TIM]
Reference(s): [8] Huerta AM., et al., 2003
[9] Maciag A., et al., 2011
[5] Metzger S., et al., 1988
[10] Nakagawa A., et al., 2006
TF binding sites (TFBSs)
[HipAB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal HipAB1 repressor relAp1 2913809 2913842 5.0 tatagtttatGTATCCTGTAACCCTGCAACGCTGGCTCGGGATAgcgaagcgtt nd [BPP], [GEA] [11]
[HipB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal HipB1 repressor relAp1 2913809 2913842 5.0 tatagtttatGTATCCTGTAACCCTGCAACGCTGGCTCGGGATAgcgaagcgtt nd [BPP], [GEA] [11]
Note(s): 1HipB represses relA expression, and HipA enhances this repression through direct interaction with HipB, increasing its expression 36.8%, significantly higher than that by HipB alone Lin CY,2013.1HipB represses relA expression, and HipA enhances this repression through direct interaction with HipB, increasing its expression 36.8%, significantly higher than that by HipB alone Lin CY,2013.1HipB represses relA expression, and HipA enhances this repression through direct interaction with HipB, increasing its expression 36.8%, significantly higher than that by HipB alone Lin CY,2013.
2HipB represses relA expression, and HipA enhances this repression through direct interaction with HipB, increasing its expression 36.8%, significantly higher than that by HipB alone Lin CY,2013.


Transcription unit          
Name: relA-mazEF
Gene(s): mazF, mazE, relA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [4] Masuda Y., et al., 1993
[5] Metzger S., et al., 1988
Promoter
Name: relAp2
+1: 2914277
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 626
Sequence: ttttcgcattctgaaggcctggatctgtatctcgcccccgatagtgagatactcgaaaccGtctctggtgagatgccctgg
                         -35                    -10         +1                   
Note(s): Production of RelA is controlled by two promoters, relAp1 and relAp2. relAp1 is a constitutive promoter, which is mainly responsible for RelA production during log phase. relAp2, which is fine-tuned by the global regulators CRP, H-NS, and RpoS, is induced temporarily at the transition state between the exponential growth and stationary phases. Both promoters are required for maximal accumulation of RelA during stationary phase. Although relAp2 expression is partially repressed by RpoS after mid-log phase, this negative effect could be due to the RNA polymerase competition Nakagawa A,2006. However, this could also be an indirect effect.
Evidence: [CV(SM/TIM)]
[HTTIM]
[ICWHO]
[SM]
[TIM]
Reference(s): [8] Huerta AM., et al., 2003
[9] Maciag A., et al., 2011
[10] Nakagawa A., et al., 2006
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator relAp2 2914327 2914348 -60.5 agatcgcgaaAAACTGGAACGCTTTTCGCATTCtgaaggcctg nd [APIORCISFBSCS], [BPP], [SM] [10]
[H-NS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 activator relAp2 nd nd nd nd nd [BPP], [GEA], [IGI] [10]
Note(s): 1Although H-NS cannot activate relAp2 by itself, it can positively regulate relAp2 activity together with CRP, since H-NS induces conformational changes in the relAp2 transcriptional region that facilitate the CRP binding Nakagawa A,2006.2Although H-NS cannot activate relAp2 by itself, it can positively regulate relAp2 activity together with CRP, since H-NS induces conformational changes in the relAp2 transcriptional region that facilitate the CRP binding Nakagawa A,2006.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation relAp2 nd The positive effect of ppGpp on RelA is through its effect on the kcat' and not the Km. This effect is amplified by ribosomal protein L11 and deacylated RNAPhe and mRNA Goodman C.,2012 [IMP] [12]
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [12] Goodman C. 2012


Transcription unit          
Name: relA
Gene(s): relA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
Reference(s): [7] Brown DR., et al., 2014
Promoter
Name: relAp4
+1: 2914318
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 667
Sequence: ccgcaccgctaagttcggcagatcgcgaaaaactggaacgcttttcgcattctgaaggccTggatctgtatctcgcccccg
Evidence: [TIM]
Reference(s): [7] Brown DR., et al., 2014
TF binding sites (TFBSs)
[NtrC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NtrC-Pasp activator relAp4 nd nd nd nd nd [BPP], [GEA], [IGI] [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.4 2910707 2910732 cttctattctGGTCACAGGTTTCCACCTGACAGACccgcaatttt
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    

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [SM] Site mutation

 [BCE] Binding of cellular extracts

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

 [HTTIM] High-throughput transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

 [CV(SM/TIM)] cross validation(SM/TIM)

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

 [IGI] Inferred from genetic interaction


Reference(s)    

 [1] Aizenman E., Engelberg-Kulka H., Glaser G., 1996, An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death., Proc Natl Acad Sci U S A 93(12):6059-63

 [2] Gross M., Marianovsky I., Glaser G., 2006, MazG - a regulator of programmed cell death in Escherichia coli., Mol Microbiol 59(2):590-601

 [3] Marianovsky I., Aizenman E., Engelberg-Kulka H., Glaser G., 2001, The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome., J Biol Chem 276(8):5975-84

 [4] Masuda Y., Miyakawa K., Nishimura Y., Ohtsubo E., 1993, chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100., J Bacteriol 175(21):6850-6

 [5] Metzger S., Dror IB., Aizenman E., Schreiber G., Toone M., Friesen JD., Cashel M., Glaser G., 1988, The nucleotide sequence and characterization of the relA gene of Escherichia coli., J Biol Chem 263(30):15699-704

 [6] 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.

 [7] Brown DR., Barton G., Pan Z., Buck M., Wigneshweraraj S., 2014, Nitrogen stress response and stringent response are coupled in Escherichia coli., Nat Commun 5:4115

 [8] 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

 [9] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [10] Nakagawa A., Oshima T., Mori H., 2006, Identification and characterization of a second, inducible promoter of relA in Escherichia coli., Genes Genet Syst 81(5):299-310

 [11] Lin CY., Awano N., Masuda H., Park JH., Inouye M., 2013, Transcriptional repressor HipB regulates the multiple promoters in Escherichia coli., J Mol Microbiol Biotechnol 23(6):440-7

 [12] Goodman C., 2012, Regulation: positively alarming., Nat Chem Biol 8(9):738

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