RegulonDB RegulonDB 11.1: Operon Form
   

pdeL operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: pdeL
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: pdeL
Synonym(s): yahA
Gene(s): pdeL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: pdeLp2
+1: 331873
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 498
Sequence: tttattgaatgttttaaatattgtttttattggcattgctataatattggttatcatttgCtgaatggattcagtcttaat
                              -35                   -10     +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
Reference(s): [2] Huerta AM., et al., 2003
[1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[PdeL,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PdeL activator pdeLp2 331672 331696 -189.0 gttgcgaatgTTCAATAAGTTTAGTCTTATTTAATgtaaatattg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-CHIP-SEQ-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3]


Transcription unit          
Name: pdeL
Synonym(s): yahA
Gene(s): pdeL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: pdeLp1
+1: 332039
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 332
Sequence: ctatgtgtttatgagggagaggtattttcagttgatctggattgttaaattcatataatgCgcctttgctcatgaatggat
                      -35                          -10      +1                   
Evidence: [COMP-HINF]
[EXP-IDA]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [4] Maciag A., et al., 2011
[1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor pdeLp1 331871 331888 -159.5 ggttatcattTGCTGAATGGATTCAGTCttaatgagtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1]
proximal Cra repressor pdeLp1 332017 332034 -13.5 cagttgatctGGATTGTTAAATTCATATaatgcgcctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]


Transcription unit       
Name: pdeL
Gene(s): pdeL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: pdeLp3
+1: 332043
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 328
Sequence: gtgtttatgagggagaggtattttcagttgatctggattgttaaattcatataatgcgccTttgctcatgaatggatgcca
                                                  -10       +1                   
Note(s): Based on ChIp-chip analysis, it was shown that H-NS plays a role in pdeL expression Uyar E, Kurokawa K, Yoshimura M, Ishikawa S, Ogasawara N, Oshima T,2009
Transcription directed across H-NS binding regions relieves H-NS-mediated (and H-NS/StpA-mediated) repression of promoters such as proVp3, pdeLp3, and appYp2, and there is a correlation between transcription across the H-NS-bound region and derepression where RNA polymerase is able to remodel the H-NS complex and/or dislodge H-NS from the DNA and thus relieve repression Rangarajan AA,2018
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Rangarajan AA., et al., 2018


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

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

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

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping


Reference(s)    

 [1] Shimada T., Fujita N., Maeda M., Ishihama A., 2005, Systematic search for the Cra-binding promoters using genomic SELEX system., Genes Cells 10(9):907-18

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] 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

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [5] Rangarajan AA., Schnetz K., 2018, Interference of transcription across H-NS binding sites and repression by H-NS., Mol Microbiol 108(3):226-239

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