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AgaR DNA-binding transcriptional repressor

Synonyms: AgaR
Summary:
"N-acetylgalactosamine repressor," AgaR, negatively controls the expression of the aga gene cluster, which is involved in transport and catabolism of N-acetylgalactosamine and d-galactosamine [1, 3] It is negatively autoregulated and coordinately represses transcription of the divergent agaZVWEFA operon, which is related to transport and degradation of N-acetylgalactosamine [1] This repressor responds to N-acetylgalactosamine and d-galactosamine in the medium. As a member of the DeoR/GlpR family of transcriptional regulators [1] AgaR features an N-terminal domain containing a helix-turn-helix motif and a C-terminal domain that includes the key residues involved in co-inducer recognition and oligomerization [1] In accordance with other helix-turn-helix DNA-binding repressors, AgaR may bind to DNA as a tetramer. Although AgaR represses transcription it appears to be able to stabilize the RNApol, but it causes a slow rate of promoter escape [4] AgaR binds in tandem to several repeat sequences in the intergenic regions of agaZp, agaRp, and agaSp to repress transcription by overlapping the -35 and -10 boxes.
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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
AgaR Functional   nd nd nd
Evolutionary Family: DeoR
TFBs length: 20
TFBs symmetry: direct-repeat
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: agaR
  Genome position: 3277856-3278665
  Length: 810 bp / 269 aa
Operon name: agaR
TU(s) encoding the TF:
Transcription unit        Promoter
agaR
agaRp


Regulon       
Regulated gene(s) agaA, agaB, agaC, agaD, agaI, agaR, agaS, agaV, agaW, kbaY, kbaZ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Phosphotransferase Systems (PEP-dependent PTS) (5)
carbon compounds (2)
metabolism (1)
amino sugar conversions (1)
Transcription related (1)
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Regulated operon(s) agaR, agaS-kbaY-agaBCDI, kbaZ-agaVWA
First gene in the operon(s) agaR, agaS, kbaZ
Simple and complex regulons AgaR
AgaR,CRP
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AgaR,-](3)


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
  AgaR repressor agaRp Sigma70 -19.5 -57.5 agaR
tgggcttgcaTTTGCTTAATAGAAAGGCGTtaataggcaa
 3278713 3278732 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  AgaR repressor agaRp Sigma70 8.5 -30.5 agaR
cgttaataggCAAAACGAAATGAAACGAAAgttttacgaa
 3278686 3278705 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  AgaR repressor agaSp Sigma70 -274.5 -361.5 agaS, kbaY, agaB, agaC, agaD, agaI
ctggattcagGGTCAATTAGCTTCGTTTTGatagtttgct
 3281605 3281624 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  AgaR repressor agaSp Sigma70 -211.5 -298.5 agaS, kbaY, agaB, agaC, agaD, agaI
ccgtaaggccTTTCTTTTTCTTTCGTTTTGatctgtgcag
 3281668 3281687 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  AgaR repressor agaSp Sigma70 -94.5 -181.5 agaS, kbaY, agaB, agaC, agaD, agaI
gcatccagcaATCCCTTTTGCTTCCTTTATcttttctttc
 3281785 3281804 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  AgaR repressor agaSp Sigma70 -52.5 -139.5 agaS, kbaY, agaB, agaC, agaD, agaI
cgatcacaaaTTTCGTTTTATTTCTTTTTTctccattgaa
 3281827 3281846 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  AgaR repressor agaSp Sigma70 -21.5 -108.5 agaS, kbaY, agaB, agaC, agaD, agaI
tccattgaacTTTCAGTTTCTTTTCTATAGattttaatca
 3281858 3281877 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  AgaR repressor agaSp Sigma70 22.5 -65.5 agaS, kbaY, agaB, agaC, agaD, agaI
aaagacatcaCCAAGTGAAATGAAACGAAAggcaagtgaa
 3281901 3281920 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  AgaR repressor kbaZp Sigma70 -75.5 -123.5 kbaZ, agaV, agaW, agaA
tttcagtgacTTTCATTATGTTTCTTTTGTgaatcagatc
 3278781 3278800 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2]
  AgaR repressor kbaZp Sigma70 -31.5 -79.5 kbaZ, agaV, agaW, agaA
aaccattatcTTTCGTTTTATTTTTATCTCaccatgacgc
 3278825 3278844 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  AgaR repressor kbaZp Sigma70 3.5 -45.5 kbaZ, agaV, agaW, agaA
tgacgcagtaTCAACTGAAACAAAACGAAAgattaatatc
 3278859 3278878 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]


Alignment and PSSM for AgaR TFBSs    

Aligned TFBS of AgaR   
  Sequence
  AACTTTCGTTTCATTTCGTTTTG
  GCCTTTCTTTTTCTTTCGTTTTG
  GCCTTTCGTTTCATTTCACTTGG
  AAATTTCGTTTTATTTCTTTTTT
  ATCTTTCGTTTTGTTTCAGTTGA
  GACTTTCATTATGTTTCTTTTGT
  ATCTTTCGTTTTATTTTTATCTC
  AACTTTCAGTTTCTTTTCTATAG
  CCCTTTTGCTTCCTTTATCTTTT
  CAGGGTCAATTAGCTTCGTTTTG
  GCCTTTCTATTAAGCAAATGCAA

Position weight matrix (PWM). AgaR matrix-quality result    
A	5	5	1	0	0	0	0	3	2	0	1	2	5	0	0	1	2	3	1	1	0	2	2
C	2	4	9	0	0	0	10	0	1	0	0	3	3	1	1	0	7	1	2	0	2	0	1
G	4	0	1	1	1	0	0	6	1	0	0	0	3	1	0	0	0	3	1	1	0	3	5
T	0	2	0	10	10	11	1	2	7	11	10	6	0	9	10	10	2	4	7	9	9	6	3

Consensus    
;	consensus.strict             	gcCTTTCgtTTtatTTCgttttg
;	consensus.strict.rc          	CAAAACGAAATAAAACGAAAGGC
;	consensus.IUPAC              	rmCTTTCgtTTyvtTTCktttkg
;	consensus.IUPAC.rc           	CMAAAMGAAABRAAACGAAAGKY
;	consensus.regexp             	[ag][ac]CTTTCgtTT[ct][acg]tTTC[gt]ttt[gt]g
;	consensus.regexp.rc          	C[AC]AAA[AC]GAAA[CGT][AG]AAACGAAAG[GT][CT]

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

 [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-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Ray WK., Larson TJ., 2004, Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12., Mol Microbiol 51(3):813-26

 [2] 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

 [3] Brinkkotter A., Kloss H., Alpert C., Lengeler JW., 2000, Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli., Mol Microbiol 37(1):125-35

 [4] Guharajan S, Chhabra S, Parisutham V, Brewster RC, 2021, Quantifying the regulatory role of individual transcription factors in Escherichia coli., Cell Rep, 37(6):109952 10.1016/j.celrep.2021.109952

 [5] Reizer J., Ramseier TM., Reizer A., Charbit A., Saier MH., 1996, Novel phosphotransferase genes revealed by bacterial genome sequencing: a gene cluster encoding a putative N-acetylgalactosamine metabolic pathway in Escherichia coli., Microbiology 142 ( Pt 2):231-50


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