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GalS DNA-binding transcriptional dual regulator

Synonyms: GalS, GalS-D-galactose
Summary:
The "Galactose isorepressor," GalS, is a DNA-binding transcription factor that represses transcription of the operons involved in transport and catabolism of D-galactose [1, 2, 3, 4, 5]. Synthesis of these operons is induced when E. coli is grown in the presence of the inducer (D-galactose) and the absence glucose [1, 2, 4, 5] GalS is negatively autoregulated, and its expression is increased in the presence of inducer and glucose [1, 2] On the other hand, GalS is highly homologous in its amino acid sequence to GalR (55% identical and 88% similar); apparently both act together and are capable of cross-talking to regulate expression of the gal regulon [1, 4] For this reason these regulators bind the same operators, in the cis regulatory regions, with different affinities. In the presence of an inductor, GalS undergoes a conformational change that reduces its affinity for the operator.
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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
GalS Functional   Apo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IPI] S [1], [2]
GalS-D-galactose Functional Allosteric Holo nd nd nd
Evolutionary Family: GalR/LacI
TFBs length: 16
TFBs symmetry: inverted-repeat
Sensing class: Sensing external and internal signals
Connectivity class: Local Regulator
Gene name: galS
  Genome position: 2240628-2241668
  Length: 1041 bp / 346 aa
Operon name: galS
TU(s) encoding the TF:
Transcription unit        Promoter
galS
galSp


Regulon       
Regulated gene(s) galE, galK, galM, galP, galR, galS, galT, mglA, mglB, mglC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (10)
colanic acid (M antigen) (3)
galactose metabolism (3)
capsule (M and K antigens) (3)
membrane (2)
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Regulated operon(s) galETKM, galP, galR, galS, mglBAC
First gene in the operon(s) galE, galP, galR, galS, mglB
Simple and complex regulons CRP,FlhDC,GalR,GalS
CRP,GalR,GalS
CRP,GalR,GalS,H-NS,HU
CRP,GalR,GalS,HU
CRP,GalR,GalS,NagC
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[GalS,-](8)
[GalS,+](1)


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
  GalS repressor galEp Sigma38 -60.5 -86.5 galE, galT, galK, galM
ctaaattcttGTGTAAACGATTCCACtaatttattc
 792134 792149 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [5]
  GalS repressor galEp Sigma38 52.5 26.5 galE, galT, galK, galM
tctggttaccGGTGGTAGCGGTTACAttggaagtca
 792022 792037 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [4], [5]
  GalS repressor galEp1 Sigma70 -60.5 -86.5 galE, galT, galK, galM
ctaaattcttGTGTAAACGATTCCACtaatttattc
 792134 792149 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [5]
  GalS repressor galEp1 Sigma70 52.5 26.5 galE, galT, galK, galM
tctggttaccGGTGGTAGCGGTTACAttggaagtca
 792022 792037 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [4], [5]
  GalS repressor galEp2 Sigma70 -55.5 -86.5 galE, galT, galK, galM
ctaaattcttGTGTAAACGATTCCACtaatttattc
 792134 792149 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [5]
  GalS-D-galactose activator galEp2 Sigma70 -55.5 -86.5 galE, galT, galK, galM
ctaaattcttGTGTAAACGATTCCACtaatttattc
 792134 792149 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [4], [5]
  GalS repressor galEp2 Sigma70 57.5 26.5 galE, galT, galK, galM
tctggttaccGGTGGTAGCGGTTACAttggaagtca
 792022 792037 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [2], [3], [4], [4], [5]
  GalS-D-galactose repressor galPp Sigma70 -243.5 -272.5 galP
atcatcacaaCTGAAACCGATTACACcaaccacaac
 3088004 3088019 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [6]
  GalS-D-galactose repressor galPp Sigma70 -207.5 -236.5 galP
agacaaagatTTGTAATATTTTCATAttattattcg
 3088040 3088055 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  GalS-D-galactose repressor galPp Sigma70 -178.5 -207.5 galP
ttattcggttTTCACAGTTGTTACATttcttttcag
 3088069 3088084 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [6]
  GalS-D-galactose repressor galPp Sigma70 -107.5 -136.5 galP
tgatgatataACTCAATTATTTTCATgcacttaaat
 3088140 3088155 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [6]
  GalS repressor galPp Sigma70 -61.5 -90.5 galP
ataaatgttaGTGTAAGCGATTACACtgatgtgatt
 3088186 3088201 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [3], [5], [6], [6]
  GalS repressor galPp Sigma70 136.5 107.5 galP
cctggatatcGGTGTAATTGCTGGCGcactgccgtt
 3088383 3088398 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [3], [5], [6], [6]
  GalS-D-galactose repressor galRp Sigma70 8.5 -22.5 galR
cactgaaagaATGTAAGCGTTTACCCactaaggtat
 2976569 2976584 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [3]
  GalS repressor galSp Sigma70 -61.5 -103.5 galS
aacaaaacggCTGTAACCGTTTCCATtgctgtgact
 2241764 2241779 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [2], [2], [3]
  GalS repressor galSp Sigma70 92.5 50.5 galS
tggcgtctctGTGGCAACGGTTTCCCgggtgctcaa
 2241611 2241626 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [2], [2], [3]
  GalS repressor mglBp Sigma70 -59.5 -277.5 mglB, mglA, mglC
aaatcaggcgATGTAACCGCTTTCAAtctgtgagtg
 2240618 2240633 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1], [2], [3], [4], [4], [5], [7]
  GalS repressor mglBp2 Sigma38 -59.5 -277.5 mglB, mglA, mglC
aaatcaggcgATGTAACCGCTTTCAAtctgtgagtg
 2240618 2240633 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1], [2], [3], [4], [4], [5], [7]


Alignment and PSSM for GalS TFBSs    

Aligned TFBS of GalS   
  Sequence
  TTAGTGGAATCGTTTACAC
  TTAGTGTAAGCGATTACAC
  AGATTGAAAGCGGTTACAT
  GCAATGGAAACGGTTACAG
  AGAATGTAAGCGTTTACCC
  CCGGTGGTAGCGGTTACAT
  TTGGTGTAATCGGTTTCAG
  TCTGTGGCAACGGTTTCCC
  AGTGCGCCAGCAATTACAC
  AGATTTGTAATATTTTCAT
  ATAACTCAATTATTTTCAT
  GTTTTCACAGTTGTTACAT

Position weight matrix (PWM). GalS matrix-quality result    
A	5	0	7	3	0	0	2	7	12	3	0	3	2	0	0	8	0	10	0
C	1	3	0	0	2	1	2	3	0	0	9	0	0	0	0	0	12	2	5
G	2	4	2	6	0	9	5	0	0	6	0	8	6	0	0	0	0	0	2
T	4	5	3	3	10	2	3	2	0	3	3	1	4	12	12	4	0	0	5

Consensus    
;	consensus.strict             	agagtGgaAgCGgTTaCAc
;	consensus.strict.rc          	GTGTAACCGCTTCCACTCT
;	consensus.IUPAC              	wbagtGgmAgCGkTTwCAy
;	consensus.IUPAC.rc           	RTGWAAMCGCTKCCACTVW
;	consensus.regexp             	[at][cgt]agtGg[ac]AgCG[gt]TT[at]CA[ct]
;	consensus.regexp.rc          	[AG]TG[AT]AA[AC]CGCT[GT]CCACT[ACG][AT]

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-IDA] Inferred from direct assay

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

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

 [EXP-IPI] Inferred from physical interaction

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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


Reference(s)    

 [1] Geanacopoulos M., Adhya S., 1997, Functional characterization of roles of GalR and GalS as regulators of the gal regulon., J Bacteriol 179(1):228-34

 [2] Weickert MJ., Adhya S., 1993, Control of transcription of gal repressor and isorepressor genes in Escherichia coli., J Bacteriol 175(1):251-8

 [3] Semsey S., Krishna S., Sneppen K., Adhya S., 2007, Signal integration in the galactose network of Escherichia coli., Mol Microbiol 65(2):465-76

 [4] Weickert MJ., Adhya S., 1992, Isorepressor of the gal regulon in Escherichia coli., J Mol Biol 226(1):69-83

 [5] Weickert MJ., Adhya S., 1993, The galactose regulon of Escherichia coli., Mol Microbiol 10(2):245-51

 [6] El Qaidi S., Allemand F., Oberto J., Plumbridge J., 2009, Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism., Mol Microbiol 71(1):146-57

 [7] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol 178(2):183-204

 [8] Golding A, Weickert MJ, Tokeson JP, Garges S, Adhya S, 1991, A mutation defining ultrainduction of the Escherichia coli gal operon., J Bacteriol, 173(19):6294 10.1128/jb.173.19.6294-6296.1991


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