RegulonDB RegulonDB 10.9: Operon Form
   

serC-aroA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: serC
Gene(s): serC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Man TK., et al., 1997
Promoter
Name: serCp2
+1: 957579
Distance from start of the gene: 74
Sequence: tttgccctcaacggttttactcattgcgatgtgtgtcactgaatgataaaaccgatagccAcaggaataatgtattacctg
Note(s): serCp2 was validated experimentally in aerobic conditions Chung D,2013.
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [2] Chung D., et al., 2013
[3] Salgado H, et al., 2012


Transcription unit          
Name: serC
Gene(s): serC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Man TK., et al., 1997
Promoter
Name: serCp
+1: 957595
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 58
Sequence: ttactcattgcgatgtgtgtcactgaatgataaaaccgatagccacaggaataatgtattAcctgtggtcgcaatcgattg
                           -35                    -10       +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Lim CJ., et al., 1994
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
proximal CRP-cAMP1 repressor serCp 957498 957519 -86.0 agagattcttTTGTGTGATGCAAGCCACATTTTtgccctcaac nd [APIORCISFBSCS], [GEA], [SM] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 activator serCp 957454 957468 -134.0 gggtgacctgACAGTAAAAACATCGGctttttgcta nd [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [CCE], [CSE], [GEA], [SM] [1], [6], [7]
Note(s): 1It is important to note that the CRP site position at the serC-aroA operon is unusual for this regulator Man TK,1997.1Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,20191Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019
2It is important to note that the CRP site position at the serC-aroA operon is unusual for this regulator Man TK,1997.


Transcription unit          
Name: serC-aroA
Gene(s): serC, aroA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The serC-aroA operon codes for a transaminase of the PLP pathway and a synthase of the common aromatic synthesis pathway Duncan K,1986 This operon is repressed by CRP (catabolite repression regulator) Lim CJ,1994and activated by Lrp (leucine-responsive regulator) Man TK,1997 It is possibly an attenuator regulatory mechanism for the aroA gene, as a terminator sequence between serC and aroA, and a different expression level has been observed Duncan K,1986
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [8] Duncan K., et al., 1986
[5] Lim CJ., et al., 1994
[1] Man TK., et al., 1997
Promoter
Name: serCp
+1: 957595
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 58
Sequence: ttactcattgcgatgtgtgtcactgaatgataaaaccgatagccacaggaataatgtattAcctgtggtcgcaatcgattg
                           -35                    -10       +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Lim CJ., et al., 1994
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
proximal CRP-cAMP1 repressor serCp 957498 957519 -86.0 agagattcttTTGTGTGATGCAAGCCACATTTTtgccctcaac nd [APIORCISFBSCS], [GEA], [SM] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 activator serCp 957454 957468 -134.0 gggtgacctgACAGTAAAAACATCGGctttttgcta nd [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [CCE], [CSE], [GEA], [SM] [1], [6], [7]
Note(s): 1It is important to note that the CRP site position at the serC-aroA operon is unusual for this regulator Man TK,1997.1Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,20191Additional evidence supports this TF-gene interaction with no precise position defined.
GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019
2It is important to note that the CRP site position at the serC-aroA operon is unusual for this regulator Man TK,1997.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [9] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.5 958761 958790 ttgcttaatcCCCACAGCCAGCCTGTGGGGTTTTTATTTctgttgtaga
  anti-terminator -4.6 958728 958769 agttcgaacgCCGTCACGGTTAATGCCGAAATTTTGCTTAATCCCCACAGCcagcctgtgg
  anti-anti-terminator -12.3 958689 958744 cgctggaaggCGTTAAAGCGCTGACAGACTTCATGGTTGAGTTCGAACGCCGTCACGGTTAATGCcgaaattttg
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"




Reference(s)    

 [1] Man TK., Pease AJ., Winkler ME., 1997, Maximization of transcription of the serC (pdxF)-aroA multifunctional operon by antagonistic effects of the cyclic AMP (cAMP) receptor protein-cAMP complex and Lrp global regulators of Escherichia coli K-12., J Bacteriol 179(11):3458-69

 [2] Chung D., Park D., Myers K., Grass J., Kiley P., Landick R., Keles S., 2013, dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data., PLoS Comput Biol 9(10):e1003246

 [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] 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

 [5] Lim CJ., Hwang W., Park EH., Fuchs JA., 1994, Cyclic AMP-dependent expression of the Escherichia coli serC-aroA operon., Biochim Biophys Acta 1218(2):250-3

 [6] Cho BK., Barrett CL., Knight EM., Park YS., Palsson BO., 2008, Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli., Proc Natl Acad Sci U S A 105(49):19462-7

 [7] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [8] Duncan K., Coggins JR., 1986, The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways., Biochem J 234(1):49-57

 [9] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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