RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: serA
Synonym(s): OP00315
Gene(s): serA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The serA gene codes for 3-phosphoglycerate dehydrogenase, which catalyzes the first step in the biosynthesis of serine from glucose Tobey KL,1986. It was observed that the serA gene is repressed by the Nac protein and that there are two Nac-binding sites overlapping the serAp1 promoter Blauwkamp TA,2002 Therefore, we linked this regulation to the serAp1 promoter; however, the serAp2 promoter could be also affected by Nac. Blauwkamp TA,2002 et al. hypothesized that Nac represses serine biosynthesis, through the repression of serA, as part of a cellular mechanism to reduce metabolism when cells become starved for nitrogen. On the other hand, there is indirect evidence of Lrp regulating serA transcription (gene expression analysis) Tuan LR,1990 but no further studies have been done to prove a direct interaction.
Based on genome-wide analysis, 472 single-gene knockouts were studied to determine their anaerobic fermentation products, based on the control of redox reactions. It was determined that the combined knockout of the guaB, pyrD, serA, fnr, arcA, and arcB genes enhanced D-lactate overproduction Kim HJ,2013
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Calvo JM., et al., 1994
[2] Tobey KL., et al., 1986
[3] Tuan LR., et al., 1990
Promoter
Name: serAp1
+1: 3058456
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 46
Sequence: tcaacatcgcgacgcaaacgttcatattgccgcaatattattttttgatatgttgaaaggCggatgcaaatccgcacacaa
                           -35                   -10        +1                   
Evidence: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Yang L., et al., 2002
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
nd Lrp1 activator serAp1 nd nd nd nd nd [RSE], [BPP], [GEA], [IGI] [5], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac repressor serAp1 3058468 3058482 -19.0 atattgccgcAATATTATTTTTTGATatgttgaaag nd [RSE], [AIBSPD], [APIORCISFBSCS], [CSE], [GEA] [6], [7]
proximal Nac repressor serAp1 3058479 3058493 -30.0 cgcaaacgttCATATTGCCGCAATATtattttttga nd [APIORCISFBSCS], [GEA] [6]
Note(s): 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,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% 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,20193Additional 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| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm. GCs_GeneExpression_CONTROL: wild-type| MOPS| 0.2% glycerol| | 37.0 C| | | OD600 from 1.8 to 2.2| transition point| | |200 rpm Kroner GM,2019br>GCs_GeneExpression_EXP: lrp knockout mutant| MOPS| 0.2% 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


Transcription unit          
Name: serA
Gene(s): serA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The serA gene codes for 3-phosphoglycerate dehydrogenase, which catalyzes the first step in the biosynthesis of serine from glucose Tobey KL,1986. It was observed that the serA gene is repressed by the Nac protein and that there are two Nac-binding sites overlapping the serAp1 promoter Blauwkamp TA,2002 Therefore, we linked this regulation to the serAp1 promoter; however, the serAp2 promoter could be also affected by Nac. Blauwkamp TA,2002 et al. hypothesized that Nac represses serine biosynthesis, through the repression of serA, as part of a cellular mechanism to reduce metabolism when cells become starved for nitrogen. On the other hand, there is indirect evidence of Lrp regulating serA transcription (gene expression analysis) Tuan LR,1990 but no further studies have been done to prove a direct interaction
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [2] Tobey KL., et al., 1986
Promoter
Name: serAp2
+1: 3058549
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 139
Sequence: gtgtcacgcttttaccaggcaattgtcgattgctctaaataaatcctctaaaccagcataTtcatccaagaattacctttg
                              -35                     -10   +1                   
Evidence: [HIPP]
[ICWHO]
[IMP]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Yang L., et al., 2002
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-cAMP activator serAp2 3058618 3058639 -80.0 tcccccgttaAAAAAATTCTCTTCATTAAATTTggtgacatgt nd [APIORCISFBSCS], [GEA] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp-L-leucine repressor serAp2 nd nd nd nd nd [BPP], [GEA], [IGI] nd




Reference(s)    

 [1] Calvo JM., Matthews RG., 1994, The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli., Microbiol Rev 58(3):466-90

 [2] Tobey KL., Grant GA., 1986, The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase., J Biol Chem 261(26):12179-83

 [3] Tuan LR., D'Ari R., Newman EB., 1990, The leucine regulon of Escherichia coli K-12: a mutation in rblA alters expression of L-leucine-dependent metabolic operons., J Bacteriol 172(8):4529-35

 [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] Yang L., Lin RT., Newman EB., 2002, Structure of the Lrp-regulated serA promoter of Escherichia coli K-12., Mol Microbiol 43(2):323-33

 [6] Blauwkamp TA., Ninfa AJ., 2002, Nac-mediated repression of the serA promoter of Escherichia coli., Mol Microbiol 45(2):351-63

 [7] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [8] 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)


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