RegulonDB RegulonDB 9.4: Operon Form
   

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




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


Transcription unit          
Name: glnLG
Synonym(s): OP00034
Gene(s): glnG, glnL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [1] Miranda-Rios J., et al., 1987
[2] Ueno-Nishio S., et al., 1983
[3] Ueno-Nishio S., et al., 1984
Promoter
Name: glnLp
+1: 4056371
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: ttttctccgtcaattctctgatgcttcgcgctttttatccgtaaaaagctataatgcactAaaatggtgcaacctgttcag
                         -35                      -10       +1                   
Evidence: [TIM]
Reference(s): [2] Ueno-Nishio S., et al., 1983
[3] Ueno-Nishio S., et al., 1984
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
proximal NtrC-Phosphorylated repressor glnLp 4056361 4056377 3.0 aaagctataaTGCACTAAAATGGTGCAacctgttcag nd [BPP], [HIBSCS], [SM] [3], [4]


Transcription unit          
Name: glnALG
Synonym(s): OP00034, glnA
Gene(s): glnG, glnL, glnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is mainly expressed under nitrogen limitation; therefore, the internal terminator of glnALG is active under this condition |CITS: [2865194]|.
The NtrC regulator binds to five sites upstream of glnAp2. In a phosphorylated state and at low nitrogen concentrations, the NtrC protein (NtrC-P) increases its affinity for specific DNA-binding sites, which are represented by a 17-bp inverted repeat sequence (TGCACCn5GGTGCA) |CITS: [3304660], [2871943]|.
NtrC-P at low concentrations of nitrogen binds strongly to sites -140 and -108, used for repression of the glnA promoter glnAp1, and weakly to sites -90, -68, and -45. Therefore, the recognition of NtrC at the sites -140 and -108 plays an important role in its interaction with Eσ54 and the activation of transcription at glnAp2 |CITS: [3304660], [2871943], [2571609]|.
On the other hand, the recognition of NtrC-P to the sites -90, -68, and -45 appears to increase the local concentration of NRI-phosphate at glnAp2, which does not seem to contribute significantly in the activation at glnAp2 |CITS: [3304660], [2871943]|.
Under nitrogen-rich growth conditions, the expression of the glnA and glnG genes increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the three promoters that transcribe the genes could be regulated by the regulators |CITS:[21272324]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
Reference(s): [5] Magasanik B. 1989
[1] Miranda-Rios J., et al., 1987
[6] Sasse-Dwight S., et al., 1988
Promoter
Name: glnAp2
+1: 4058107
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 73
Sequence: gcatgataacgccttttaggggcaatttaaaagttggcacagatttcgctttatctttttTacggcgacacggccaaaata
                                   -24         -12          +1                   
Evidence: [TIM]
Reference(s): [7] Ninfa AJ., et al., 1987
[8] Reitzer LJ., et al., 1989
[9] Tian ZX., et al., 2001
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
proximal CRP-cAMP repressor glnAp2 4058152 4058173 -55.5 ttttgcacgaTGGTGCGCATGATAACGCCTTTtaggggcaat nd [AIBSCS], [BPP], [GEA] [9]
proximal CRP-cAMP repressor glnAp2 4058154 4058175 -57.5 ccttttgcacGATGGTGCGCATGATAACGCCTtttaggggca nd [AIBSCS], [BPP], [GEA] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator glnAp2 4058155 4058169 -55.0 gcacgatggtGCGCATGATAACGCCttttaggggc nd [AIBSCS], [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NtrC-Phosphorylated activator glnAp2 4058144 4058160 -45.0 tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd [GEA], [HIBSCS] [11], [13]
proximal NtrC-Phosphorylated activator glnAp2 4058167 4058183 -68.0 ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd [GEA], [HIBSCS], [SM] [11], [13]
proximal NtrC-Phosphorylated activator glnAp2 4058188 4058204 -89.0 ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [10], [11], [13]
remote NtrC-Phosphorylated activator glnAp2 4058207 4058223 -108.0 tttccattgaAGCACTATATTGGTGCAacattcacat nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]
remote NtrC-Phosphorylated activator glnAp2 4058239 4058255 -140.0 caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [10], [11], [12]


Transcription unit          
Name: glnA
Gene(s): glnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is mainly expressed under nitrogen limitation; therefore, the internal terminator of glnALG is active under this condition |CITS: [2865194]|.
The NtrC regulator binds to five sites upstream of glnAp2. In a phosphorylated state and at low nitrogen concentrations, the NtrC protein (NtrC-P) increases its affinity for specific DNA-binding sites, which are represented by a 17-bp inverted repeat sequence (TGCACCn5GGTGCA) |CITS: [3304660], [2871943]|.
NtrC-P at low concentrations of nitrogen binds strongly to sites -140 and -108, used for repression of the glnA promoter glnAp1, and weakly to sites -90, -68, and -45. Therefore, the recognition of NtrC at the sites -140 and -108 plays an important role in its interaction with Eσ54 and the activation of transcription at glnAp2 |CITS: [3304660], [2871943], [271609]|.
On the other hand, the recognition of NtrC-P to the sites -90, -68, and -45 appears to increase the local concentration of NRI-phosphate at glnAp2, which does not seem to contribute significantly in the activation at glnAp2 |CITS: [3304660], [2871943]|.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [4] Rocha M., et al., 1985
Promoter
Name: glnAp2
+1: 4058107
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 73
Sequence: gcatgataacgccttttaggggcaatttaaaagttggcacagatttcgctttatctttttTacggcgacacggccaaaata
                                   -24         -12          +1                   
Evidence: [TIM]
Reference(s): [7] Ninfa AJ., et al., 1987
[8] Reitzer LJ., et al., 1989
[9] Tian ZX., et al., 2001
Terminator(s)
Type: rho-independent
Sequence: ttcctgacttAAGCGGCGCTGGTTATCCATcggagccatc
Reference(s): [4] Rocha M., et al., 1985
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
proximal CRP-cAMP repressor glnAp2 4058152 4058173 -55.5 ttttgcacgaTGGTGCGCATGATAACGCCTTTtaggggcaat nd [AIBSCS], [BPP], [GEA] [9]
proximal CRP-cAMP repressor glnAp2 4058154 4058175 -57.5 ccttttgcacGATGGTGCGCATGATAACGCCTtttaggggca nd [AIBSCS], [BPP], [GEA] [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator glnAp2 4058155 4058169 -55.0 gcacgatggtGCGCATGATAACGCCttttaggggc nd [AIBSCS], [BPP], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NtrC-Phosphorylated activator glnAp2 4058144 4058160 -45.0 tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd [GEA], [HIBSCS] [11], [13]
proximal NtrC-Phosphorylated activator glnAp2 4058167 4058183 -68.0 ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd [GEA], [HIBSCS], [SM] [11], [13]
proximal NtrC-Phosphorylated activator glnAp2 4058188 4058204 -89.0 ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [10], [11], [13]
remote NtrC-Phosphorylated activator glnAp2 4058207 4058223 -108.0 tttccattgaAGCACTATATTGGTGCAacattcacat nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]
remote NtrC-Phosphorylated activator glnAp2 4058239 4058255 -140.0 caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [10], [11], [12]


Transcription unit          
Name: glnA
Gene(s): glnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is mainly expressed under nitrogen limitation; therefore, the internal terminator of glnALG is active under this condition |CITS: [2865194]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [4] Rocha M., et al., 1985
Promoter
Name: glnAp1
+1: 4058222
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 188
Sequence: gcataaaaagggttatccaaaggtcattgcaccaacatggtgcttaatgtttccattgaaGcactatattggtgcaacatt
                       -35                   -10            +1                   
Evidence: [TIM]
Reference(s): [9] Tian ZX., et al., 2001
Terminator(s)
Type: rho-independent
Sequence: ttcctgacttAAGCGGCGCTGGTTATCCATcggagccatc
Reference(s): [4] Rocha M., et al., 1985
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
proximal CRP-cAMP activator glnAp1 4058283 4058304 -71.5 ttgcagagtcCCTTTGTGATCGCTTTCACGGAgcataaaaag nd [HIBSCS] [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-Phosphorylated repressor glnAp1 4058144 4058160 71.0 tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd [GEA], [HIBSCS] [11], [13]
remote NtrC-Phosphorylated repressor glnAp1 4058167 4058183 48.0 ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd [GEA], [HIBSCS], [SM] [11], [13]
proximal NtrC-Phosphorylated repressor glnAp1 4058188 4058204 27.0 ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [13]
proximal NtrC-Phosphorylated repressor glnAp1 4058207 4058223 8.0 tttccattgaAGCACTATATTGGTGCAacattcacat nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]
proximal NtrC-Phosphorylated repressor glnAp1 4058239 4058255 -25.0 caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]


Transcription unit          
Name: glnALG
Synonym(s): OP00034
Gene(s): glnG, glnL, glnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the glnA and glnG genes increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the three promoters that transcribe the genes could be regulated by the regulators |CITS:[21272324]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
Reference(s): [1] Miranda-Rios J., et al., 1987
Promoter
Name: glnAp1
+1: 4058222
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 188
Sequence: gcataaaaagggttatccaaaggtcattgcaccaacatggtgcttaatgtttccattgaaGcactatattggtgcaacatt
                       -35                   -10            +1                   
Evidence: [TIM]
Reference(s): [9] Tian ZX., et al., 2001
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
proximal CRP-cAMP activator glnAp1 4058283 4058304 -71.5 ttgcagagtcCCTTTGTGATCGCTTTCACGGAgcataaaaag nd [HIBSCS] [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NtrC-Phosphorylated repressor glnAp1 4058144 4058160 71.0 tgcgcatgatAACGCCTTTTAGGGGCAatttaaaagt nd [GEA], [HIBSCS] [11], [13]
remote NtrC-Phosphorylated repressor glnAp1 4058167 4058183 48.0 ggtgcagcccTTTTGCACGATGGTGCGcatgataacg nd [GEA], [HIBSCS], [SM] [11], [13]
proximal NtrC-Phosphorylated repressor glnAp1 4058188 4058204 27.0 ttggtgcaacATTCACATCGTGGTGCAgcccttttgc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [13]
proximal NtrC-Phosphorylated repressor glnAp1 4058207 4058223 8.0 tttccattgaAGCACTATATTGGTGCAacattcacat nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]
proximal NtrC-Phosphorylated repressor glnAp1 4058239 4058255 -25.0 caaaggtcatTGCACCAACATGGTGCTtaatgtttcc nd [BPP], [GEA], [HIBSCS], [SM] [7], [8], [11], [12]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [15] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.5 4056426 4056452 agctatctgtAGCCCATCTCTGCATGGGCTTTTTTCtccgtcaatt
  anti-terminator -3.9 4056443 4056489 cggagcaggtGAGTCGCTCTCCAACGTGAAGTTTGTCAGCTATCTGTAGCCCATCTctgcatgggc
  anti-anti-terminator -28.11 4056464 4056543 cggatgcgacGCAAATGCGTCTTATCCGGCCTACACGGTGATGATGTGGTAGGCCGGAGCAGGTGAGTCGCTCTCCAACGTGAAGTTTGtcagctatct
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"




Reference(s)    

 [1] Miranda-Rios J., Sanchez-Pescador R., Urdea M., Covarrubias AA., 1987, The complete nucleotide sequence of the glnALG operon of Escherichia coli K12., Nucleic Acids Res. 15(6):2757-70

 [2] Ueno-Nishio S., Backman KC., Magasanik B., 1983, Regulation at the glnL-operator-promoter of the complex glnALG operon of Escherichia coli., J Bacteriol. 153(3):1247-51

 [3] Ueno-Nishio S., Mango S., Reitzer LJ., Magasanik B., 1984, Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli., J Bacteriol. 160(1):379-84

 [4] Rocha M., Vazquez M., Garciarrubio A., Covarrubias AA., 1985, Nucleotide sequence of the glnA-glnL intercistronic region of Escherichia coli., Gene. 37(1-3):91-9

 [5] Magasanik B., 1989, Regulation of transcription of the glnALG operon of Escherichia coli by protein phosphorylation., Biochimie NIL:71(9-10):1005-12

 [6] Sasse-Dwight S., Gralla JD., 1988, Probing the Escherichia coli glnALG upstream activation mechanism in vivo., Proc Natl Acad Sci U S A. 85(23):8934-8

 [7] Ninfa AJ., Reitzer LJ., Magasanik B., 1987, Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers., Cell. 50(7):1039-46

 [8] Reitzer LJ., Movsas B., Magasanik B., 1989, Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase., J Bacteriol. 171(10):5512-22

 [9] Tian ZX., Li QS., Buck M., Kolb A., Wang YP., 2001, The CRP-cAMP complex and downregulation of the glnAp2 promoter provides a novel regulatory linkage between carbon metabolism and nitrogen assimilation in Escherichia coli., Mol Microbiol. 41(4):911-24

 [10] Collado-Vides J., Magasanik B., Gralla JD., 1991, Control site location and transcriptional regulation in Escherichia coli., Microbiol Rev. 55(3):371-94

 [11] Reitzer LJ., Magasanik B., 1985, Expression of glnA in Escherichia coli is regulated at tandem promoters., Proc Natl Acad Sci U S A. 82(7):1979-83

 [12] Reitzer LJ., Magasanik B., 1986, Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter., Cell. 45(6):785-92

 [13] Atkinson MR., Pattaramanon N., Ninfa AJ., 2002, Governor of the glnAp2 promoter of Escherichia coli., Mol Microbiol. 46(5):1247-57

 [14] Huo YX., Nan BY., You CH., Tian ZX., Kolb A., Wang YP., 2006, FIS activates glnAp2 in Escherichia coli: role of a DNA bend centered at -55, upstream of the transcription start site., FEMS Microbiol Lett. 257(1):99-105

 [15] Merino E, Yanofsky C,, 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet 21(5):260-4


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