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YjjQ DNA-binding transcriptional repressor

Synonyms: YjjQ
Summary:
YjjQ is a transcriptional repressor of genes required for flagellar synthesis, capsule formation, and other genes related to virulence [1] Repression is mediated by binding to a palindromic DNA motif. Episomal expression of yjjQ inhibits motility and biofilm formation [1] YjjQ harbors a FixJ/NarL-type C-terminal helix-turn-helix DNA-binding domain [2]. YjjQ may play a role in detoxification of methylglyoxal (MG) and dihydroxyacetone (DHA) [3]. YjjQ belongs to the LuxR family of transcriptional regulators. The orthologous protein in avian pathogenic E. coli [4] and in Salmonella enterica serovar Typhimurium [5] may play a role in virulence. A yjjQ insertion mutant increases the sensitivity of a gloA mutant to MG and DHA.
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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
YjjQ Functional   nd nd nd
Evolutionary Family: LuxR/UhpA
TFBs length: 15
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: yjjQ
  Genome position: 4603477-4604202
  Length: 726 bp / 241 aa
Operon name: yjjQ-bglJ
TU(s) encoding the TF:
Transcription unit        Promoter
yjjQ-bglJ
yjjQp


Regulon       
Regulated gene(s) dgcN, flhC, flhD, gfcA, ompC, ybhL, yciX, yfiB, yfiR, ymiA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (4)
flagellum (2)
Transcription related (2)
activator (2)
repressor (2)
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Regulated operon(s) flhDC, gfcA, ompC, ybhL, yfiR-dgcN-yfiB, ymiA-yciX
First gene in the operon(s) flhD, gfcA, ompC, ybhL, yfiR, ymiA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
CpxR,EnvY,IHF,Lrp,OmpR,YjjQ
YjjQ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YjjQ,-](6)


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
  YjjQ repressor flhDp Sigma70 11.0 -188.0 flhD, flhC
ttgcgtcgatTTAGGAAAAATCTTAgataagtgta
 1978378 1978392 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [1], [1]
  YjjQ repressor gfcAp Sigma70 -49.0 -1007.0 gfcA
atagctttcgTAACAATTTCCTTATctttaatttg
 1050744 1050758 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  YjjQ repressor gfcAp Sigma70 -16.0 -974.0 gfcA
tgtattttgcTAAGATTTATCTTATgctcacaagt
 1050711 1050725 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [1], [1]
  YjjQ repressor ompCp1 Sigma70 -64.0 -145.0 ompC
ctatagcgatAAATGAAACATCTTAaaagttttag
 2312887 2312901 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  YjjQ repressor ybhLp Sigma70 2.0 -25.0 ybhL
gcagtatcctTAAGATATTCCTTATatcttcagga
 819852 819866 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  YjjQ repressor yfiRp Sigma70 -65.0 -116.0 yfiR, dgcN, yfiB
aaattaaacaTAAGATTTTACTCATtgtgttttat
 2741752 2741766 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  YjjQ repressor ymiAp Sigma70 -6.0 -64.0 ymiA, yciX
aaagtttcttTAGGATTTGTCTCATcgtatgatta
 1335077 1335091 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]


Alignment and PSSM for YjjQ TFBSs    

Aligned TFBS of YjjQ   
  Sequence
  TAAGATATTCCTTATATC
  TAAGATTTTTCCTAAATC
  TAAGATTTTACTCATTGT
  TAAGATTTATCTTATGCT
  TAGGATTTGTCTCATCGT
  TAACAATTTCCTTATCTT
  TAAGATGTTTCATTTATC

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

Consensus    
;	consensus.strict             	TAaGAttTttCttatatc
;	consensus.strict.rc          	GATATAAGAAAAATCTTA
;	consensus.IUPAC              	TAaGAttTtyCtyatmky
;	consensus.IUPAC.rc           	RMKATRAGRAAAATCTTA
;	consensus.regexp             	TAaGAttTt[ct]Ct[ct]at[ac][gt][ct]
;	consensus.regexp.rc          	[AG][AC][GT]AT[AG]AG[AG]AAAATCTTA

PWM logo   


 


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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Wiebe H., Gurlebeck D., Gross J., Dreck K., Pannen D., Ewers C., Wieler LH., Schnetz K., 2015, YjjQ Represses Transcription of flhDC and Additional Loci in Escherichia coli., J Bacteriol 197(16):2713-20

 [2] Venkatesh GR., Kembou Koungni FC., Paukner A., Stratmann T., Blissenbach B., Schnetz K., 2010, BglJ-RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS., J Bacteriol 192(24):6456-64

 [3] Kim I., Kim J., Min B., Lee C., Park C., 2007, Screening of genes related to methylglyoxal susceptibility., J Microbiol 45(4):339-43

 [4] Li G, Laturnus C, Ewers C, Wieler LH, 2005, Identification of genes required for avian Escherichia coli septicemia by signature-tagged mutagenesis., Infect Immun, 73(5):2818 10.1128/IAI.73.5.2818-2827.2005

 [5] Lawley TD, Chan K, Thompson LJ, Kim CC, Govoni GR, Monack DM, 2006, Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse., PLoS Pathog, 2(2):e11 10.1371/journal.ppat.0020011

 [6] Stratmann T., Madhusudan S., Schnetz K., 2008, Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO., J Bacteriol 190(3):926-35


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