RegulonDB RegulonDB 11.1: Operon Form
   

puuA-ymjE-puuP operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: puuA-ymjE-puuP
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: puuP
Synonym(s): ycjJ
Gene(s): puuP, ymjE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: puuPp
+1: 1359373
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 32
Sequence: gtaatccagacatttcccggatgtcgcgttatggagcgcgggcggcaacgggcttccgttAacgattaagactgtgacgag
                                     -24        -12         +1                   
Note(s): This promoter was identified by microarray and ChIP assays with a mutant
σ54 strain and a σ54-overexpressing strain,
and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Reitzer L., et al., 2001
[3] Zhao K., et al., 2010


Transcription unit          
Name: puuAP
Gene(s): puuP, ymjE, puuA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of puuA is induced by putrescine and overexpressed by upon deletion of puuR Kurihara S,2008.
All puu genes, including puuA and puuD, may could be synchronistically regulated by PuuR and/or other regulators, such as ArcA and FNR, which repressed the expression of puuA under anaerobic conditions Kurihara S,2008.
Putrescine is catabolized by products of the puu gene cluster, which that are regulated by ArcA, FNR, and PuuR to decrease the toxicity of putrescine and to utilize putrescine as both a nitrogen and carbon sources Kurihara S,2008.
The puuA gene is downregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The curator has determined that the binding sites of PuuR may have a length of 20 nucleotides with an inverted repeated symmetry (ATGGaCAATATATTGaCCAT). The sequence proposed by Nemoto et al. in 2012 was included in these regions Nemoto N,2012. Nemoto et al. proposed binding sites that are 15 nucleotides long, with an asymmetric recognition sequence, AAAATATAATGAACA Nemoto N,2012.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [4] Nemoto N., et al., 2012
Promoter
Name: puuAp
+1: 1360968
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 60
Sequence: tcatttttgcaaactcaatttaacatttgacaaacatttagtttgcatacagattcgaatGgtggtcattatattttacgc
                                -35                  -10    +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [5] Gama-Castro S., et al., 2008
[6] Maciag A., et al., 2011
[4] Nemoto N., et al., 2012
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor puuAp 1361126 1361140 -165.0 cgataaccggATTGTTCATTATATTttccatgctc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[FNR,-] 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
proximal FNR repressor puuAp 1360933 1360946 29.0 attttacgctTTGATAACGAGCGGaaaacaaacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[PuuR,-] 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
proximal PuuR repressor puuAp 1360948 1360967 11.5 gattcgaatgGTGGTCATTATATTTTACGCtttgataacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4], [8], [9]
proximal PuuR repressor puuAp 1361043 1361062 -84.5 aatgacctttATGTTCAATATTTTTTCAATctagcagtgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4], [8], [9]
remote PuuR repressor puuAp 1361085 1361104 -126.5 atctcacaaaGTGGACTAAATTATCGCCATtactgcgctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] C [4], [8], [9]
remote PuuR repressor puuAp 1361120 1361139 -161.5 gataaccggaTTGTTCATTATATTTTCCATgctcaatctc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4], [8], [9]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP] Inferred from expression pattern

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

 [EXP-IMP] Inferred from mutant phenotype

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

 [IC] Inferred by curator

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [3] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [4] Nemoto N., Kurihara S., Kitahara Y., Asada K., Kato K., Suzuki H., 2012, Mechanism for regulation of the putrescine utilization pathway by the transcription factor PuuR in Escherichia coli K-12., J Bacteriol 194(13):3437-47

 [5] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [6] 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

 [7] Partridge JD., Scott C., Tang Y., Poole RK., Green J., 2006, Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions., J Biol Chem 281(38):27806-15

 [8] Kurihara S., Oda S., Tsuboi Y., Kim HG., Oshida M., Kumagai H., Suzuki H., 2008, gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12., J Biol Chem 283(29):19981-90

 [9] Kurihara S., Tsuboi Y., Oda S., Kim HG., Kumagai H., Suzuki H., 2009, The putrescine Importer PuuP of Escherichia coli K-12., J Bacteriol 191(8):2776-82

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