RegulonDB RegulonDB 11.2:Regulon Page
   

PdeL DNA-binding transcriptional dual regulator

Synonyms: PdeL
Summary:
PdeL is a c-di-GMP-specific phosphodiesterase consisting of an N-terminal LuxR-like DNA-binding domain and a C-terminal EAL domain that is required for phosphodiesterase activity [5]. The isolated EAL domain of the enzyme is in a fast monomer-dimer equilibrium. Only the dimeric form of PdeL has phosphodiesterase activity, and substrate binding increases dimerization affinity [6]. Crystal structures of the EAL domain alone and in various complexes have been solved, showing structural coupling between the dimer interface and the catalytic site [6]. A screen for suppressors of the motility defect of a |FRAME: EG12252 ΔpdeH| mutant identified activating mutations in E. coli's alternative c-di-GMP phosphodiesterases (PDEs), including PdeL. This supports a model whereby the signaling specificity of PDEs is the result of environmental signals required for their activation. Suppressor mutations in pdeL consisted of point mutations that are located within its catalytic EAL domain and resulted in higher levels of PdeL protein, increased enzymatic activity, reduced levels of intracellular c-di-GMP, and increased swimming motility [2].
Read more >


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
PdeL Functional   nd nd nd
Evolutionary Family: LuxR/UhpA
TFBs length: 24
Connectivity class: Local Regulator
Gene name: pdeL
  Genome position: 332371-333459
  Length: 1089 bp / 362 aa
Operon name: pdeL
TU(s) encoding the TF:
Transcription unit        Promoter
pdeL
pdeLp1
pdeL
pdeLp2
pdeL
pdeLp3


Regulon       
Regulated gene(s) fliF, fliG, fliH, fliI, fliJ, fliK, pdeL
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
flagella (6)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (5)
flagellum (4)
ATP proton motive force interconversion (1)
regulation (1)
Regulated operon(s) fliFGHIJK, pdeL
First gene in the operon(s) fliF, pdeL
Simple and complex regulons CsgD,FlhDC,PdeL
PdeL
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PdeL,+](1)
[PdeL,-](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
  PdeL repressor fliFp1 Sigma70 nd nd fliF, fliG, fliH, fliI, fliJ, fliK
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  PdeL activator pdeLp2 Sigma70 -189.0 -687.0 pdeL
gttgcgaatgTTCAATAAGTTTAGTCTTATTTAATgtaaatattg
 331672 331696 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-CHIP-SEQ-MANUAL], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [2], [2], [3], [4]



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
  PdeL activator yghJ Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
  PdeL repressor rfe Gene nd
ggcgttttgcTTTTATATCTGTAATCTTAATGccgcgctggc
3967722 3967743 3967732.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


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

 [COMP-HINF] Inferred by a human based on computational evidence

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

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


Reference(s)    

 [1] Yilmaz C., Rangarajan AA., Schnetz K., 2020, The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli., J Bacteriol

 [2] Reinders A., Hee CS., Ozaki S., Mazur A., Boehm A., Schirmer T., Jenal U., 2015, Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli., J Bacteriol 198(3):448-62

 [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] Sellner B., Prakapaite R., van Berkum M., Heinemann M., Harms A., Jenal U., 2021, A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection., mBio 12(6):e0324621

 [5] Schmidt AJ, Ryjenkov DA, Gomelsky M, 2005, The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains., J Bacteriol, 187(14):4774 10.1128/JB.187.14.4774-4781.2005

 [6] Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T, 2014, Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP., J Biol Chem, 289(10):6978 10.1074/jbc.M113.516195

 [7] Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P, 2016, Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli., J Bacteriol, 198(1):7 10.1128/JB.00424-15

 [8] Hengge R, 2016, Trigger phosphodiesterases as a novel class of c-di-GMP effector proteins., Philos Trans R Soc Lond B Biol Sci, 371(1707):None 10.1098/rstb.2015.0498


RegulonDB