RegulonDB RegulonDB 10.7:Regulon Page

XynR DNA-binding transcriptional dual regulator

Synonyms: XynR-D-xylonate, XynR
Based on SELEX screening of Escherichia coli K-12 W3110, XynR, formerly known as YagI, was identified as a regulator of xylonate catabolism; it is a rare single-target TF, and its regulation network is still fixed within the CR4-6 prophage without significant cross-talk with the host. It regulates the bidirectional transcripts yagA(b) and yagEF(GH) [1]. A single peak of XynR binding was identified within the spacer of bidirectional transcription units of the yagA and yagEF operons. However, by decreasing the cutoff of detection, approximately 30 low-level peaks were detected, which are all located inside open reading frames (ORFs) [1]. The level of XynR was detectable in the exponential growth phase, but it decreased to an undetectable level during growth in the stationary phase [1]. A xynR mutant shows increased biofilm formation compared to wild type, but a lower increase in biofilm formation when the derepressed conjugative plasmid R1drd19 is present [3]. XynR: xylonate catabolism regulator [1] Read more >

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
XynR Non-Functional   Apo nd nd
XynR-D-xylonate Functional   Holo nd nd
Connectivity class: Local Regulator
Gene name: xynR
  Genome position: 288404-289162
  Length: 759 bp / 252 aa
Operon name: xynR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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 (Confirmed, Strong, Weak) References

High-throughput Transcription factor binding sites (TFBSs)

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  XynR-D-xylonate repressor nd nd nd 282236 282255 nd [BPP], [GEA], [GS], [ICWHO] [1], [2]
  XynR-D-xylonate repressor nd nd nd 282236 282255 nd [BPP], [GEA], [GS], [ICWHO] [1], [2]

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



 [1] Shimada T., Momiyama E., Yamanaka Y., Watanabe H., Yamamoto K., Ishihama A., 2017, Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12., FEMS Microbiol Lett 364(22)

 [2] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [3] Yang X, Ma Q, Wood TK, 2008, The R1 conjugative plasmid increases Escherichia coli biofilm formation through an envelope stress response., Appl Environ Microbiol, 2008 May