RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: proVWX
Synonym(s): proU
Gene(s): proV, proW, proX   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analysis it was concluded that FNR represses proVWX operon expression under anaerobiosis. A putative FNR-binding site, which was not reported in the paper, was identified upstream of this operon, but it is still not known which of the three promoters (proUp1, proUp2, or proUp3) is affected by FNR Salmon K,2003.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for proW . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Dattananda CS., et al., 1989
[2] Gowrishankar J. 1989
Promoter
Name: proVp
+1: 2804563
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 252
Sequence: taattcccgccaaatagctttttatcacgcaaataatttgtggtgatctacactgatactCtgttgcattattcgcctgaa
                          -35               -10             +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Gowrishankar J. 1989
[3] Huerta AM., et al., 2003
[4] Rajkumari K., et al., 1996
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor proVp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [6]


Transcription unit          
Name: proVWX
Synonym(s): proU
Gene(s): proV, proW, proX   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analysis it was concluded that FNR represses proVWX operon expression under anaerobiosis. A putative FNR-binding site, which was not reported in the paper, was identified upstream of this operon, but it is still not known which of the three promoters (proUp1, proUp2, or proUp3) is affected by FNR Salmon K,2003.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for proW . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Dattananda CS., et al., 1989
[2] Gowrishankar J. 1989
Promoter
Name: proVp1
+1: 2804563
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 252
Sequence: taattcccgccaaatagctttttatcacgcaaataatttgtggtgatctacactgatactCtgttgcattattcgcctgaa
                      -35                        -10        +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Gowrishankar J. 1989
[3] Huerta AM., et al., 2003
[4] Rajkumari K., et al., 1996
TF binding sites (TFBSs)
[H-NS,-] 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
nd H-NS repressor proVp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5], [6]


Transcription unit       
Name: proVWX
Synonym(s): proU
Gene(s): proV, proW, proX   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analysis it was concluded that FNR represses proVWX operon expression under anaerobiosis. A putative FNR-binding site, which was not reported in the paper, was identified upstream of this operon, but it is still not known which of the three promoters (proUp1, proUp2, or proUp3) is affected by FNR Salmon K,2003.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for proW . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Reference(s): [1] Dattananda CS., et al., 1989
[2] Gowrishankar J. 1989
Promoter
Name: proVp2
+1: 2804599
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 216
Sequence: tttgtggtgatctacactgatactctgttgcattattcgcctgaaaccacaatattcaggCgttttttcgctatctttgac
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Gowrishankar J. 1989
[3] Huerta AM., et al., 2003
[4] Rajkumari K., et al., 1996


Transcription unit          
Name: proVWX
Synonym(s): proU
Gene(s): proV, proW, proX   Genome Browser M3D Gene expression COLOMBOS
Note(s): By making use of microarray analysis it was concluded that FNR represses proVWX operon expression under anaerobiosis. A putative FNR-binding site, which was not reported in the paper, was identified upstream of this operon, but it is still not known which of the three promoters (proUp1, proUp2, or proUp3) is affected by FNR Salmon K,2003.
IHF is a trans-acting factor implicated directly in the regulation of the proVWX operon Khodr A,2015 IHF helps to relieve H-NS repression of the proVWX operon in an off state rather than by acting as an activation factor Khodr A,2015
Regulation of both H-NS and IHF on proVp3 suggests a model where, instead of preventing or helping transcription by steric hindrance, there is modification of the local structure of the nucleic acid that offers a substrate for the polymerase that is optimized or not for initiation of transcription, depending on the environmental conditions Khodr A,2015
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for proW . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Dattananda CS., et al., 1989
[2] Gowrishankar J. 1989
Promoter
Name: proVp3
+1: 2804755
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 60
Sequence: ttcatgccacatttgccatcaggggttgcctcagattctcagtatgttagggtagaaaaaAgtgactatttccattgggta
                          -35                   -10         +1                   
Note(s): Expression of the proVWX operon is osmo-regulated and repressed by H-NS at low-osmolarity but not at high-osmolarity conditions Bouffartigues E, Buckle M, Badaut C, Travers A, Rimsky S,2007
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-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Gowrishankar J. 1989
[3] Huerta AM., et al., 2003
[7] Rangarajan AA., et al., 2018
TF binding sites (TFBSs)
[H-NS,-] 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 H-NS repressor proVp3 2804715 2804729 -33.0 atttgccatcAGGGGTTGCCTCAGAttctcagtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5], [6]
proximal H-NS repressor proVp3 2804754 2804768 7.0 gggtagaaaaAAGTGACTATTTCCAttgggtaata nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
proximal H-NS repressor proVp3 2804773 2804787 26.0 tttccattggGTAATATATCGACATagacaaataa nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804792 2804806 45.0 cgacatagacAAATAAAGGAATCTTtctattgcat nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804819 2804833 72.0 tattgcatggCAATTAAATTAGAAAttaaaaatct nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804831 2804845 84.0 attaaattagAAATTAAAAATCTTTataaaatatt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804847 2804861 100.0 aaaatctttaTAAAATATTTGGCGAgcatccacag nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804877 2804891 130.0 cacagcgagcGTTCAAATATATCGAacaaggactt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804903 2804917 156.0 caaggactttCAAAAGAACAAATTCtggaaaaaac nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
remote H-NS repressor proVp3 2804917 2804931 170.0 agaacaaattCTGGAAAAAACTGGGctatcgcttg nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4], [5], [6]
[IHF,+] 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 IHF activator proVp3 2804730 2804744 -18.5 ttgcctcagaTTCTCAGTATGTTAGggtagaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]
remote IHF activator proVp3 2804887 2804902 140.0 gttcaaatatATCGAACAAGGACTTTcaaaagaaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.5 2804576 2804607 tgcattattcGCCTGAAACCACAATATTCAGGCGTTTTTTCgctatctttg
  anti-terminator -3.17 2804544 2804579 ataatttgtgGTGATCTACACTGATACTCTGTTGCATTATTCGCCtgaaaccaca
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

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

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

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

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


Reference(s)    

 [1] Dattananda CS., Gowrishankar J., 1989, Osmoregulation in Escherichia coli: complementation analysis and gene-protein relationships in the proU locus., J Bacteriol 171(4):1915-22

 [2] Gowrishankar J., 1989, Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli., J Bacteriol 171(4):1923-31

 [3] 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

 [4] Rajkumari K., Kusano S., Ishihama A., Mizuno T., Gowrishankar J., 1996, Effects of H-NS and potassium glutamate on sigmaS- and sigma70-directed transcription in vitro from osmotically regulated P1 and P2 promoters of proU in Escherichia coli., J Bacteriol 178(14):4176-81

 [5] Lucht JM., Dersch P., Kempf B., Bremer E., 1994, Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli., J Biol Chem 269(9):6578-8

 [6] Rajkumari K., Gowrishankar J., 2001, In vivo expression from the RpoS-dependent P1 promoter of the osmotically regulated proU operon in Escherichia coli and Salmonella enterica serovar Typhimurium: activation by rho and hns mutations and by cold stress., J Bacteriol 183(22):6543-50

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

 [8] Khodr A., Fairweather V., Bouffartigues E., Rimsky S., 2015, IHF is a trans-acting factor implicated in the regulation of the proU P2 promoter., FEMS Microbiol Lett 362(3):1-6

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