RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit          
Name: puuDRCBE
Gene(s): puuD, puuR, puuC, puuB, puuE   Genome Browser M3D Gene expression COLOMBOS
Note(s): PuuR repress the expression of puuD Kurihara S,2005
The expression of puuD is induced by putrescine and O2; and reduced by succinate or NH4Cl Kurihara S, Oda S, Kumagai H, Suzuki H,2006
The expression of puuD is repressed at the exponential phase Kurihara S, Oda S, Kumagai H, Suzuki H,2006and in an anaerobic environment Kang Y,2005; and it is induced at the stationary phase Kurihara S, Oda S, Kumagai H, Suzuki H,2006
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
A novel strain that overexpresses puuC under the control of a strong promoter led to lower rates of glycerol accumulation and higher 3-hydroxypropionic acid (3-HP) production. The PuuR transcription factor was also inactivated, producing the same results. Combined, these strategies further improved 3-HP yield with a concomitant reduction in glycerol accumulation, and the engineered strain, JHS_Δgypr-PT7, produced 53.7 g/L 3-HP and 1.5 g/L glycerol Lee TY, Min WK, Kim HJ, Seo JH,2020
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Nemoto N., et al., 2012
Promoter
Name: puuDp
+1: 1361052
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 68
Sequence: atgtttgtcaaatgttaaattgagtttgcaaaaatgaaaacccactgctagattgaaaaaAtattgaacataaaggtcatt
                          -35                    -10        +1                   
Evidence: [HTTIM]    
[IEP]
[IMP]
[TIM]
Reference(s): [2] Maciag A., et al., 2011
[3] Mendoza-Vargas A., et al., 2009
[1] Nemoto N., et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-phosphorylated repressor puuDp 1361126 1361140 82.0 gagcatggaaAATATAATGAACAATccggttatcg nd [AIBSCS], [GEA], [AIBSCS] [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP repressor puuDp 1361104 1361126 63.5 atttagtccaCTTTGTGAGATTGAGCATGGAAAatataatgaa nd [IEP], [APIORCISFBSCS] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PuuR repressor puuDp 1360948 1360967 -94.5 cgttatcaaaGCGTAAAATATAATGACCACcattcgaatc nd [GEA], [IC], [BPP], [IC] [1], [4], [5]
proximal PuuR repressor puuDp 1361043 1361062 1.5 ccactgctagATTGAAAAAATATTGAACATaaaggtcatt nd [GEA], [IC], [BPP], [IC] [1], [4], [5]
remote PuuR repressor puuDp 1361085 1361104 43.5 aagcgcagtaATGGCGATAATTTAGTCCACtttgtgagat nd [GEA], [IC], [BPP], [IC], [SM] [1], [4], [5]
remote PuuR repressor puuDp 1361120 1361139 78.5 gagattgagcATGGAAAATATAATGAACAAtccggttatc nd [GEA], [IC], [BPP], [IC] [1], [4], [5]


Transcription unit       
Name: puuCBE
Gene(s): puuC, puuB, puuE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
[ITCR] Inferred through co-regulation
Reference(s): [2] Maciag A., et al., 2011
Promoter
Name: puuCp
+1: 1362728
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 15
Sequence: catacggcccggggatctctgcgccctgacgttcacaaactgcatatatctgatagacgtGaaacaggagtcataatgaat
                                                 -10        +1                   
Evidence: [HTTIM]
[IEP]
[IHBCE]
Reference(s): [2] Maciag A., et al., 2011




Reference(s)    

 [1] 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

 [2] 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

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] 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

 [5] 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

 [6] Terui Y., Saroj SD., Sakamoto A., Yoshida T., Higashi K., Kurihara S., Suzuki H., Toida T., Kashiwagi K., Igarashi K., 2014, Properties of putrescine uptake by PotFGHI and PuuP and their physiological significance in Escherichia coli., Amino Acids 46(3):661-70

 [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] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74


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