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YhaJ DNA-binding transcriptional activator

Synonyms: YhaJ
Summary:
YhaJ is a member of the LysR protein family. It was previously associated with regulation of virulence in an enterohemorrhagic Escherichia coli (EHEC) strain [3]. Its capability to bind to the promoter regions of several genes in E. coli and regulate their activity has been demonstrated [1]. YhaJ dosage varied drastically between four evolutionarily distinct E. coli strains, including enterohemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), and the nonpathogenic commensal K-12, grown in minimal essential medium (MEM). In contrast, growth in rich medium (LB), which naturally enhances YhaJ expression levels, yielded almost identical expression levels of YhaJ in all strains [2]. Increased YhaJ expression levels between minimal and rich media correlated with an increase in the number of global YhaJ binding sites [2]. The regulatory network of YhaJ is surprisingly heterogenous despite its highly conserved nature across the E.
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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
YhaJ Functional   nd nd nd
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yhaJ
  Genome position: 3253318-3254214
  Length: 897 bp / 298 aa
Operon name: yhaJ
TU(s) encoding the TF:
Transcription unit        Promoter
yhaJ
 


Regulon       
Regulated gene(s) bssS
Multifun term(s) of regulated gene(s)
information transfer (1)
Regulated operon(s) bssS
First gene in the operon(s) bssS
Simple and complex regulons YhaJ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YhaJ,+](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
  YhaJ activator bssSp1 Sigma32 nd nd bssS
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  YhaJ activator ybiJ Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  YhaJ activator ygiD Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  YhaJ activator yqjF Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  YhaJ activator yhaKL Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  YhaJ activator yhhW Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  YhaJ activator yhaJ Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-PCR-MANUAL] W [2]


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

 [EXP-CHIP-PCR-MANUAL] ChIP-PCR evidence used in manual assertion


Reference(s)    

 [1] Palevsky N., Shemer B., Connolly JP., Belkin S., 2016, The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation., Front Microbiol 7:1490

 [2] Connolly JPR., O'Boyle N., Roe AJ., 2020, Widespread Strain-Specific Distinctions in Chromosomal Binding Dynamics of a Highly Conserved Escherichia coli Transcription Factor., mBio 11(3)

 [3] Connolly JP, Gabrielsen M, Goldstone RJ, Grinter R, Wang D, Cogdell RJ, Walker D, Smith DG, Roe AJ, 2016, A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence., PLoS Pathog, 12(1):e1005359 10.1371/journal.ppat.1005359

 [4] O'Boyle N, Turner NCA, Roe AJ, Connolly JPR, 2020, Plastic Circuits: Regulatory Flexibility in Fine Tuning Pathogen Success., Trends Microbiol, 28(5):360 10.1016/j.tim.2020.01.002

 [5] Connolly JPR, O'Boyle N, Turner NCA, Browning DF, Roe AJ, 2019, Distinct intraspecies virulence mechanisms regulated by a conserved transcription factor., Proc Natl Acad Sci U S A, 116(39):19695 10.1073/pnas.1903461116

 [6] Wan B, Zhang Q, Ni J, Li S, Wen D, Li J, Xiao H, He P, Ou HY, Tao J, Teng Q, Lu J, Wu W, Yao YF, 2017, Type VI secretion system contributes to Enterohemorrhagic Escherichia coli virulence by secreting catalase against host reactive oxygen species (ROS)., PLoS Pathog, 13(3):e1006246 10.1371/journal.ppat.1006246

 [7] Journet L, Cascales E, 2016, The Type VI Secretion System in Escherichia coli and Related Species., EcoSal Plus, 7(1):None 10.1128/ecosalplus.ESP-0009-2015


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