RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: gcvTHP
Synonym(s): OP00232, gcv
Gene(s): gcvP, gcvH, gcvT   Genome Browser M3D Gene expression COLOMBOS
Note(s): The gcvTHP operon is expressed at a higher level in LB medium than in minimal medium. Glycine enhances its expression under minimal medium conditions Yang D,2020.
Based on gene expression analysis, it was shown that CsgD could positively regulate gcvTHP expression Herrington MB,2013
Reference(s): [1] Okamura-Ikeda K., et al., 1993
[2] Stauffer LT., et al., 1994
Promoter
Name: gcvTp
+1: 3050772
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 105
Sequence: atgtgatgatcaattttaccttatggttaacagtctgtttcggtggtaagttcaggcaaaAgagaacgattgcgttgggga
                       -35                     -10          +1                   
Note(s): gcvTp is a class III activator-dependent promoter (where multiple activator molecules typically bind more than 90 bp upstream of the RNA polymerase-binding site) Stauffer LT,2005
Evidence: [ICWHO]
[TIM]
Reference(s): [3] Huerta AM., et al., 2003
[1] Okamura-Ikeda K., et al., 1993
[4] Stauffer LT., et al., 1993
[5] Stauffer LT., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: atctgactaaAAAGGCGCCGAAGCGCCTTTagaaaatagt
Reference(s): [2] Stauffer LT., 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
remote CRP-cAMP activator gcvTp 3050907 3050929 -145.5 tgtcttattcAAATTGACTTTCTCATCACATCAtctttgtata nd [APIORCISFBSCS], [BPP], [GEA], [SM] [6]
remote CRP-cAMP activator gcvTp 3051075 3051097 -313.5 tcctctgttgTTTATTTGATACCCATCACACTTtcatctcccg nd [APIORCISFBSCS], [BPP], [GEA], [SM] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator gcvTp nd nd nd nd nd [BPP], [GEA], [IGI] [19]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GcvA1 activator gcvTp 3050991 3051005 -226.0 tccgttttcgCATTATATTTTCTAATgccattattt nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [7], [8], [9], [10], [11], [12], [13], [14]
remote GcvA2 activator gcvTp 3051023 3051037 -258.0 attttcctcaTTTGAAATAAACTAATttcacctccg nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [7], [8], [9], [10], [11], [12], [13], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GcvA repressor gcvTp 3050809 3050823 -44.0 taatgtgatgATCAATTTTACCTTATggttaacagt nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [IC], [SM] [7], [9], [12], [14], [17]
proximal GcvA repressor gcvTp 3050831 3050845 -66.0 tttgcattttTTAACCATAAGCTAATgtgatgatca nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [7], [9], [12], [14], [17]
remote GcvA3 repressor gcvTp 3050991 3051005 -226.0 tccgttttcgCATTATATTTTCTAATgccattattt nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [7], [8], [9], [10], [11], [12], [13], [14]
remote GcvA4 repressor gcvTp 3051023 3051037 -258.0 attttcctcaTTTGAAATAAACTAATttcacctccg nd [APIORCISFBSCS], [BCE], [BPP], [GEA], [SM] [7], [8], [9], [10], [11], [12], [13], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 activator gcvTp 3050926 3050940 -161.0 agctcttaatATTGTCTTATTCAAATtgactttctc nd [RSE], [CSE], [GEA], [SM] [15], [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PurR-hypoxanthine repressor gcvTp 3050758 3050773 7.5 agttcaggcaAAAGAGAACGATTGCGTtggggaccgg nd [AIBSCS], [APIORCISFBSCS], [GEA] [14], [18]
Note(s): 1By making use of microarray analyses it was concluded that anarobiosis does not affect expression of the gcv operon, although FNR appears to activate it. A putative FNR-binding site, which was not shown in the report, was identified upstream of this operon Salmon K,2003.1GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
2GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,20053GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
4GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,20051Lrp takes part in gcv operon regulation as a modulator of the GcvA effect. It bends the DNA upstream of the transcription start position to allow GcvA to function Stauffer LT,1999
Additional 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,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 2.3 to 2.7| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 2.3 to 2.7| transition point| | |200 rpm Kroner GM,20192GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
3GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
4GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
5GcvA interacts with the RNA polymerase α-subunit to activate gcvTp Stauffer LT,2005
6Lrp takes part in gcv operon regulation as a modulator of the GcvA effect. It bends the DNA upstream of the transcription start position to allow GcvA to function Stauffer LT,1999
Additional 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,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol, 0.2% leucine, 0.2% isoleucine, 0.2% valine| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 0.15 to 0.25| exponential phase| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 2.3 to 2.7| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.4% glycerol, ACGU, EZ| | 37.0 C| | | OD600 from 2.3 to 2.7| transition point| | |200 rpm Kroner GM,2019
11By making use of microarray analyses it was concluded that anarobiosis does not affect expression of the gcv operon, although FNR appears to activate it. A putative FNR-binding site, which was not shown in the report, was identified upstream of this operon Salmon K,2003.


Transcription unit       
Name: gcvP
Gene(s): gcvP   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [20] Zaslaver A., et al., 2006
Promoter
Name: gcvPp
+1: Unknown
Evidence: [IEP]
Reference(s): [20] Zaslaver A., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: atctgactaaAAAGGCGCCGAAGCGCCTTTagaaaatagt
Reference(s): [2] Stauffer LT., et al., 1994




Reference(s)    

 [1] Okamura-Ikeda K., Ohmura Y., Fujiwara K., Motokawa Y., 1993, Cloning and nucleotide sequence of the gcv operon encoding the Escherichia coli glycine-cleavage system., Eur J Biochem 216(2):539-48

 [2] Stauffer LT., Fogarty SJ., Stauffer GV., 1994, Characterization of the Escherichia coli gcv operon., Gene 142(1):17-22

 [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] Stauffer LT., Ghrist A., Stauffer GV., 1993, The Escherichia coli gcvT gene encoding the T-protein of the glycine cleavage enzyme system., DNA Seq 3(6):339-46

 [5] Stauffer LT., Stauffer GV., 1994, Characterization of the gcv control region from Escherichia coli., J Bacteriol 176(20):6159-64

 [6] Wonderling LD., Stauffer GV., 1999, The cyclic AMP receptor protein is dependent on GcvA for regulation of the gcv operon., J Bacteriol 181(6):1912-9

 [7] Jourdan AD., Stauffer GV., 1999, Genetic analysis of the GcvA binding site in the gcvA control region., Microbiology 145 ( Pt 8):2153-62

 [8] Jourdan AD., Stauffer GV., 1998, Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding., J Bacteriol 180(18):4865-71

 [9] Stauffer LT., Stauffer GV., 2005, GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon., FEMS Microbiol Lett 242(2):333-8

 [10] Stauffer LT., Stauffer GV., 1998, Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 5):1417-22

 [11] Stauffer LT., Stauffer GV., 1998, Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli., Microbiology 144 ( Pt 10):2865-72

 [12] Wilson RL., Stauffer GV., 1994, DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system., J Bacteriol 176(10):2862-8

 [13] Wilson RL., Steiert PS., Stauffer GV., 1993, Positive regulation of the Escherichia coli glycine cleavage enzyme system., J Bacteriol 175(3):902-4

 [14] Wilson RL., Urbanowski ML., Stauffer GV., 1995, DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli., J Bacteriol 177(17):4940-6

 [15] 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)

 [16] Stauffer LT., Stauffer GV., 1999, Role for the leucine-responsive regulatory protein (Lrp) as a structural protein in regulating the Escherichia coli gcvTHP operon., Microbiology 145 ( Pt 3):569-76

 [17] Wonderling LD., Urbanowski ML., Stauffer GV., 2000, GcvA binding site 1 in the gcvTHP promoter of Escherichia coli is required for GcvA-mediated repression but not for GcvA-mediated activation., Microbiology 146 ( Pt 11):2909-18

 [18] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

 [19] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [20] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8


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