RegulonDB RegulonDB 10.8: 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: [TIM]
Reference(s): [2] Jasiecki J., et al., 2006
[3] 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): [4] Cao GJ., et al., 1996
[5] Liu JD., et al., 1989
[6] Podkovyrov SM., et al., 1995
[1] Talarico TL., et al., 1992
Promoter
Name: pcnBp3
+1: 159171
Sigma Factor: Sigma70, Sigma38
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]
[TIM]
Reference(s): [7] Binns N., et al., 2002
[2] Jasiecki J., et al., 2006
[3] 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 pcnBp3 DksA weakly inhibited pcnBp3 (pB) transcription Nadratowska-Wesolowska B,2010 Pronounced impairment of pcnBp3 (pB) activity was caused by ppGpp Nadratowska-Wesolowska B,2010 A dramatic decrease in the level of pcnBp3 (pB)-derived transcripts was observed when both DksA and ppGpp were present in the reaction mixture Nadratowska-Wesolowska B,2010 [APPH]
[GEA]
[3]
  ppGpp inhibition pcnBp3   [GEA] [3]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
Reference(s): [3] 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: [TIM]
Reference(s): [2] Jasiecki J., et al., 2006
[3] 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: [TIM]
Reference(s): [3] 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 ppGpp is the main negative regulator of pcnBp4 (pS2) in vivo. DksA had little effect in inhibiting the activity of pcnBp4(pS2). However, DksA enhanced the inhibitory effect of ppGpp Nadratowska-Wesolowska B,2010 [GEA] [3]
  ppGpp inhibition pcnBp4   [GEA] [3]
Evidence: [GEA] Gene expression analysis
Reference(s): [3] 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] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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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