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YqhC DNA-binding transcriptional activator

Synonyms: YqhC
Summary:
The YqhC transcriptional activator directly binds to the promoter region of the yqhD gene, which contains the SoxS-like binding sequence as well as a 24-bp palindrome [1]. YqhC also regulates dkgA expression [2]. The yqhD and dkgA genes encode NADPH-dependent oxidoreductases, and both are involved in furfural reduction [2]. YqhC belongs to the AraC/XylS transcriptional activator family, as it shows 13.6% amino acid identity with AraC [1, 2]. The identity of the intracellular signal for YqhC is yet to be discovered [1]. Closely related bacteria contain yqhC, yqhD, and dkgA orthologs in the same arrangement as in Escherichia coli LY180. On the other hand, orthologs of yqhC are also present in more distantly related Gram-negative bacteria [2]. It is probable that YqhC regulates its own expression, since it is inducible by furfural [2, 4].
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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
YqhC Functional   nd nd nd
Evolutionary Family: AraC/XylS
TFBs length: 24
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yqhC
  Genome position: 3154262-3155218
  Length: 957 bp / 318 aa
Operon name: yqhC
TU(s) encoding the TF:
Transcription unit        Promoter
yqhC
 


Regulon       
Regulated gene(s) dkgA, yqhD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (1)
methylglyoxal metabolism (1)
protection (1)
Regulated operon(s) yqhD-dkgA
First gene in the operon(s) yqhD
Simple and complex regulons YqhC
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YqhC,+](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
  YqhC activator yqhDp Sigma70 -73.5 -126.5 yqhD, dkgA
attttgtagcATTTCTCCAGCACTCTGGAGAAATAggcaagacat
 3155217 3155241 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [3]
  YqhC activator yqhDp Sigma70 -52.5 -105.5 yqhD, dkgA
actctggagaAATAGGCAAGACATTGGCAGAAATGagcattgaga
 3155238 3155262 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION] S [1], [1], [2], [3]


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


Evidence    

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Lee C., Kim I., Lee J., Lee KL., Min B., Park C., 2010, Transcriptional activation of the aldehyde reductase YqhD by YqhC and its implication in glyoxal metabolism of Escherichia coli K-12., J Bacteriol 192(16):4205-14

 [2] Turner PC., Miller EN., Jarboe LR., Baggett CL., Shanmugam KT., Ingram LO., 2011, YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance., J Ind Microbiol Biotechnol 38(3):431-9

 [3] 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

 [4] Miller EN, Jarboe LR, Yomano LP, York SW, Shanmugam KT, Ingram LO, 2009, Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli., Appl Environ Microbiol, 75(13):4315 10.1128/AEM.00567-09

 [5] Shimada T., Ogasawara H., Kobayashi I., Kobayashi N., Ishihama A., 2021, Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12., Front Microbiol 12:697803


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