RegulonDB RegulonDB 10.10: Operon Form
   

pcnB-folK operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: pcnB-folK
Gene(s): folK, pcnB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Talarico TL., et al., 1992
Promoter
Name: pcnBp1
+1: 159151
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: caacattctcaaatgcgtcatgctgagctatgattagccgctatttttttgtcctgaatgAtgtttgacactaccgaggtg
                    -35                      -10            +1                   
Note(s): pcnBp1 and pcnBp2 may have minor roles in the pcnB-folK operon Nadratowska-Wesolowska B,2010
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Jasiecki J., et al., 2006
[4] Nadratowska-Wesolowska B., et al., 2010


Transcription unit       
Name: pcnB-folK
Gene(s): folK, pcnB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Cao GJ., et al., 1996
[6] Liu JD., et al., 1989
[7] Podkovyrov SM., et al., 1995
[1] Talarico TL., et al., 1992
Promoter
Name: pcnBp
+1: 159171
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 45
Sequence: cgagtcggcaattgtaaattcaacattctcaaatgcgtcatgctgagctatgattagccgCtatttttttgtcctgaatga
                           -35              -10             +1                   
Note(s): pcnBp3 (pB) activity is drastically impaired at the stationary phase of growth, and it is the major promoter of the pcnB-folK operon under various growth conditions Nadratowska-Wesolowska B,2010
pcnBp3 (pB) can also be weakly recognized by EσS Nadratowska-Wesolowska B,2010
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[IHBCE]
[TIM]
Reference(s): [8] Binns N., et al., 2002
[2] Huerta AM., et al., 2003
[3] Jasiecki J., et al., 2006
[4] Nadratowska-Wesolowska B., et al., 2010
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition pcnBp nd   [APPH]
[GEA]
[4]
  ppGpp inhibition pcnBp nd   [GEA] [4]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
Reference(s): [4] Nadratowska-Wesolowska B., et al., 2010


Transcription unit       
Name: pcnB-folK
Gene(s): folK, pcnB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [5] Cao GJ., et al., 1996
[6] Liu JD., et al., 1989
[7] Podkovyrov SM., et al., 1995
[1] Talarico TL., et al., 1992
Promoter
Name: pcnBp3
+1: 159171
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 45
Sequence: cgagtcggcaattgtaaattcaacattctcaaatgcgtcatgctgagctatgattagccgCtatttttttgtcctgaatga
                          -35                    -10        +1                   
Note(s): pcnBp3 (pB) activity is drastically impaired at the stationary phase of growth, and it is the major promoter of the pcnB-folK operon under various growth conditions Nadratowska-Wesolowska B,2010
pcnBp3 (pB) can also be weakly recognized by EσS Nadratowska-Wesolowska B,2010
Evidence: [HIPP]
[ICWHO]
[IDA]
[IEP]
[IHBCE]
[TIM]
Reference(s): [8] Binns N., et al., 2002
[2] Huerta AM., et al., 2003
[3] Jasiecki J., et al., 2006
[4] Nadratowska-Wesolowska B., et al., 2010


Transcription unit       
Name: pcnB-folK
Gene(s): folK, pcnB   Genome Browser M3D Gene expression COLOMBOS
Note(s): pcnBp1 and pcnBp2 may have minor roles in the pcnB-folK operon Nadratowska-Wesolowska B,2010
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Talarico TL., et al., 1992
Promoter
Name: pcnBp2
+1: 159195
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: aaactggcggcttaccgccgtgcccgagtcggcaattgtaaattcaacattctcaaatgcGtcatgctgagctatgattag
                     -35                        -10         +1                   
Evidence: [ICWHO]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Jasiecki J., et al., 2006
[4] Nadratowska-Wesolowska B., et al., 2010


Transcription unit       
Name: pcnB-folk
Gene(s): folK, pcnB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A promoter designated as pS1 was identified using primer extension by Nadratowska-Wesolowska et al. (2010); this promoter was also identified by Liu and Parkinson (1989) Nadratowska-Wesolowska B,2010. Liu JD,1989 This promoter is recognized more effectively by EσS than Eσ70; however, its transcriptional start site is 10 bp downstream of the translational start site of the pcnB gene Nadratowska-Wesolowska B,2010 The pS1 sequence bears the C residue in the -10 box, which is crucial for selective recognition of the promoter dependent on EσS Nadratowska-Wesolowska B,2010. Lacour S,2003
The pS1 promoter is active in vivo (under specific conditions) and in vitro, since there is a translation start codon, AUU, downstream of its transcriptional start site Nadratowska-Wesolowska B,2010. It is possible that there are two functional variants of PAP I, but this remains to be verified Liu JD,1989
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Talarico TL., et al., 1992
Promoter
Name: pcnBp4
+1: 159391
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 265
Sequence: aagtgccagattacattcatctgccgctggcgcttaatccacaaggcgctaaactttccaAgcagaatcatgcgcctgcgt
                           -35               -10            +1                   
Note(s): pcnBp4 (pS2) has at least two alternatives start sites, located in the region between positions -263 and -265 relative to the translation start codon, ATT Nadratowska-Wesolowska B,2010 The pS2 sequence bears the C residue in the -10 box, which is crucial for selective recognition of the promoter dependent on EσS Nadratowska-Wesolowska B,2010. Lacour S,2003
For the first time, activities have been reported for a σS-dependent promoter (pcnBp4) that is inhibited by the stringent response factors ppGpp and DksA; these findings are based on both passive and active models Nadratowska-Wesolowska B,2010
Evidence: [ICWHO]
[IDA]
[IEP]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[4] Nadratowska-Wesolowska B., et al., 2010
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition pcnBp4 nd   [GEA] [4]
  ppGpp inhibition pcnBp4 nd   [GEA] [4]
Evidence: [GEA] Gene expression analysis
Reference(s): [4] Nadratowska-Wesolowska B., et al., 2010




Reference(s)    

 [1] Talarico TL., Ray PH., Dev IK., Merrill BM., Dallas WS., 1992, Cloning, sequence analysis, and overexpression of Escherichia coli folK, the gene coding for 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase., J Bacteriol 174(18):5971-7

 [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] Jasiecki J., Wegrzyn G., 2006, Transcription start sites in the promoter region of the Escherichia coli pcnB (plasmid copy number) gene coding for poly(A) polymerase I., Plasmid 55(2):169-72

 [4] Nadratowska-Wesolowska B., Slominska-Wojewodzka M., Lyzen R., Wegrzyn A., Szalewska-Palasz A., Wegrzyn G., 2010, Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors., Mol Genet Genomics 284(4):289-305

 [5] Cao GJ., Pogliano J., Sarkar N., 1996, Identification of the coding region for a second poly(A) polymerase in Escherichia coli., Proc Natl Acad Sci U S A 93(21):11580-5

 [6] Liu JD., Parkinson JS., 1989, Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control., J Bacteriol 171(3):1254-61

 [7] Podkovyrov SM., Larson TJ., 1995, A new vector-host system for construction of lacZ transcriptional fusions where only low-level gene expression is desirable., Gene 156(1):151-2

 [8] Binns N., Masters M., 2002, Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU., Mol Microbiol 44(5):1287-98


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