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GcvA DNA-binding transcriptional dual regulator

Synonyms: GcvA-Purine, GcvA-glycine, GcvA
Summary:
"Glycine cleavage A," GcvA, is a repressor of the glycine cleavage enzyme system, which is a secondary pathway for production of C1 units [4]. It is negatively autoregulated, and it coordinately activates transcription of a small-RNA divergent gene [3, 5]. In the absence of glycine and the presence of GcvR, GcvA represses operons involved in the glycine cleavage system [3, 5, 13]. GcvR is an accessory protein that binds directly to GcvA, bending DNA to form a repression complex (GcvA/GcvR) in the regulatory region of the gcvT operon [13]. Glycine binds directly to GcvR to disrupt or block the association of the GcvA/GcvR complex, whereas purines appear to promote the formation of the repression complex through an unknown mechanism [13, 14].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
GcvA Functional   Apo nd nd nd
GcvA-Purine Non-Functional Allosteric Holo nd nd nd
GcvA-glycine Non-Functional Allosteric Holo nd nd nd
Evolutionary Family: LysR
TFBs length: 15
TFBs symmetry: inverted-repeat
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: gcvA
  Genome position: 2941650-2942567
  Length: 918 bp / 305 aa
Operon name: gcvA
TU(s) encoding the TF:
Transcription unit        Promoter
gcvA
gcvAp


Regulon       
Regulated gene(s) gcvA, gcvB, gcvH, gcvP, gcvT
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amino acids (4)
formyl-THF biosynthesis (4)
Transcription related (1)
activator (1)
repressor (1)
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Regulated operon(s) gcvA, gcvB, gcvTHP
First gene in the operon(s) gcvA, gcvB, gcvT
Simple and complex regulons CRP,FNR,GcvA,Lrp,PurR
GcvA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GcvA,+](2)
[GcvA,-](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  GcvA repressor gcvAp Sigma70 -14.0 -86.0 gcvA
agaagctcaaCGGACAATTTATAATggctcagatt
 2942646 2942660 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [2], [3], [3], [4], [5], [5], [6], [7]
  GcvA repressor gcvAp Sigma70 9.0 -64.0 gcvA
aatggctcagATTAAAAAAACTAATaggttacata
 2942624 2942638 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [3], [3], [4], [5], [5], [6], [7]
  GcvA activator gcvBp Sigma70 -65.0 -65.0 gcvB
tatgtaacctATTAGTTTTTTTAATctgagccatt
 2942624 2942638 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [3], [3], [4], [5], [5], [6], [7]
  GcvA activator gcvBp Sigma70 -43.0 -43.0 gcvB
aatctgagccATTATAAATTGTCCGttgagcttct
 2942646 2942660 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] C [1], [1], [2], [3], [3], [4], [5], [5], [6], [7]
  GcvA activator gcvTp Sigma70 -258.0 -363.0 gcvT, gcvH, gcvP
ttttcctcatTTGAAATAAACTAATttcacctccg
 3051023 3051037 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [4], [5], [5], [8], [8], [9], [10], [11]
  GcvA repressor gcvTp Sigma70 -258.0 -363.0 gcvT, gcvH, gcvP
ttttcctcatTTGAAATAAACTAATttcacctccg
 3051023 3051037 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [4], [5], [5], [8], [8], [9], [10], [11]
  GcvA activator gcvTp Sigma70 -226.0 -331.0 gcvT, gcvH, gcvP
ccgttttcgcATTATATTTTCTAATgccattattt
 3050991 3051005 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [4], [5], [5], [8], [8], [9], [10], [11]
  GcvA repressor gcvTp Sigma70 -226.0 -331.0 gcvT, gcvH, gcvP
ccgttttcgcATTATATTTTCTAATgccattattt
 3050991 3051005 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [4], [5], [5], [8], [8], [9], [10], [11]
  GcvA repressor gcvTp Sigma70 -66.0 -171.0 gcvT, gcvH, gcvP
ttgcatttttTAACCATAAGCTAATgtgatgatca
 3050831 3050845 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [4], [5], [5], [7], [12], [12]
  GcvA repressor gcvTp Sigma70 -44.0 -149.0 gcvT, gcvH, gcvP
aatgtgatgaTCAATTTTACCTTATggttaacagt
 3050809 3050823 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] C [1], [1], [2], [4], [5], [5], [7], [12], [12]


Alignment and PSSM for GcvA TFBSs    

Aligned TFBS of GcvA   
  Sequence
  TCACATTAGCTTATGGTT
  TTATATTTTCTAATGCCA
  GGACAATTTATAATGGCT
  TTAAAAAAACTAATAGGT
  TGAAATAAACTAATTTCA
  CAATTTTACCTTATGGTT

Position weight matrix (PWM). GcvA matrix-quality result    
A	0	1	6	2	5	2	2	4	2	1	0	4	6	0	1	0	0	2
C	1	1	0	2	0	0	0	0	1	5	0	0	0	0	0	1	3	0
G	1	2	0	0	0	0	0	0	1	0	0	0	0	0	4	4	1	0
T	4	2	0	2	1	4	4	2	2	0	6	2	0	6	1	1	2	4

Consensus    
;	consensus.strict             	tgAcattaaCTaATGGct
;	consensus.strict.rc          	AGCCATTAGTTAATGTCA
;	consensus.IUPAC              	tkAhawwwwCTwATGGyw
;	consensus.IUPAC.rc           	WRCCATWAGWWWWTDTMA
;	consensus.regexp             	t[gt]A[act]a[at][at][at][at]CT[at]ATGG[ct][at]
;	consensus.regexp.rc          	[AT][AG]CCAT[AT]AG[AT][AT][AT][AT]T[AGT]T[AC]A

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [IC] Inferred by curator

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

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

 [2] 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

 [3] Urbanowski ML., Stauffer LT., Stauffer GV., 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli., Mol Microbiol 37(4):856-68

 [4] 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

 [5] 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

 [6] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [7] McArthur SD., Pulvermacher SC., Stauffer GV., 2006, The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules., BMC Microbiol 6:52

 [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., 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

 [10] 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

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

 [12] 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

 [13] Ghrist AC, Heil G, Stauffer GV, 2001, GcvR interacts with GcvA to inhibit activation of the Escherichia coli glycine cleavage operon., Microbiology (Reading), 147(Pt 8):2215 10.1099/00221287-147-8-2215

 [14] Heil G, Stauffer LT, Stauffer GV, 2002, Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon., Microbiology (Reading), 148(Pt 7):2203 10.1099/00221287-148-7-2203


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