RegulonDB RegulonDB 10.6.3: Operon Form
   

glaH-lhgD-gabDTP operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: glaH-lhgD-gabDTP
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: csiD-ygaF-gabDTP
Synonym(s): csiD
Gene(s): glaH, lhgD, gabD, gabT, gabP   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is induced under stationary phase |CITS: [14731280]|, and it is part of a complex operon that contains three promoters, two of which are internal.
The glaH-lhgO-gabDTP operon is induced in stationary phase (carbon starvation) |CITS:[ 30498244]|.
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Metzner M., et al., 2004
Promoter
Name: csiDp
+1: 2788927
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 58
Sequence: ataagaaaacaatatgtcgcttttgtgcgcatttttcagaaatgtagatatttttagattAtggctacgaaatgagcatcg
                                 -35              -10       +1                   
Evidence: [TIM] ; Method: Primer Extension
[TIM]
Reference(s): [2] Marschall C., et al., 1998
[1] Metzner M., et al., 2004
TF binding sites (TFBSs)
[CRP,+] Phrase
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 csiDp 2788848 2788869 -68.5 atgttactaaTTTGTTGCTTTTGATCACAATAagaaaacaat nd [AIBSCS], [BPP], [GEA] [2], [3]
[GlaR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GlaR1 repressor csiDp 2788889 2788902 -32.0 tatgtcgcttTTGTGCGCATTTTTcagaaatgta nd [BPP], [GEA], [IEP] [1], [4]
proximal GlaR2 repressor csiDp 2788908 2788921 -13.0 tttttcagaaATGTAGATATTTTTagattatggc nd [BPP], [GEA], [IEP] [1], [4]
[H-NS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 activator csiDp nd nd nd nd nd [GEA] [3]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp-leucine1 activator csiDp nd nd nd nd nd [BPP], [GEA] [2]
Note(s): 1Repression of the glaH-lhgO-gabDTP operon by GlaR transcription factor is selectively relieved by glutarate Knorr S,2018
2Repression of the glaH-lhgO-gabDTP operon by GlaR transcription factor is selectively relieved by glutarate Knorr S,20181H-NS modulate csiD expression by influencing activation by cAMP-CRP1Lrp protects at multiple sites extending at least between positions -14 and -102. The effects of cAMP-CRP and Lrp are additive.2Repression of the glaH-lhgO-gabDTP operon by GlaR transcription factor is selectively relieved by glutarate Knorr S,2018
3Repression of the glaH-lhgO-gabDTP operon by GlaR transcription factor is selectively relieved by glutarate Knorr S,2018
4H-NS modulate csiD expression by influencing activation by cAMP-CRP
5Lrp protects at multiple sites extending at least between positions -14 and -102. The effects of cAMP-CRP and Lrp are additive.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation csiDp   [EME] [5]
Evidence: [EME] Expression microarray evidence
Reference(s): [5] Traxler MF., et al., 2008


Transcription unit       
Name: gabDTP
Gene(s): gabD, gabT, gabP   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a complex operon that contains three promoters, two of which are internal.
Although |CITS: [12446648]| et al. suggested that the csiR gene is part of the gabDTP operon because they saw a polar effect of an insertion in gabT on gabC, |CITS: [14731280]| et al. saw that the presence or absence of the gabD promoters did not affect the csiR expression and therefore concluded that the csiR gene is transcribed in another transcription unit. For this reason, this gene was not included in the operon.
The gabDTP operon is induced in response to nitrogen starvation |CITS:[30498244]|.
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Metzner M., et al., 2004
Promoter
Name: gabDp2
+1: 2790912
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 361
Sequence: gagattttgggctcgtcggggattcgccgggtgctgcaaaaccatctacgctcaggactgGgcgagatgaaaaactcgctg
                        -35               -10               +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Metzner M., et al., 2004


Transcription unit          
Name: gabDTP
Gene(s): gabD, gabT, gabP   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is part of a complex operon that contains three promoters, two of which are internal.
Although |CITS: [12446648]| et al. suggested that the csiR gene is part of the gabDTP operon because they saw a polar effect of an insertion in gabT on gabC, |CITS: [14731280]| et al. saw that the presence or absence of the gabD promoters did not affect the csiR expression and therefore concluded that the csiR gene is transcribed in another transcription unit. For this reason, this gene was not included in the operon.
The gabDTP operon is induced in response to nitrogen starvation |CITS:[30498244]|.
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Metzner M., et al., 2004
[6] Schneider BL., et al., 2002
Promoter
Name: gabDp1
+1: 2791172
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 101
Sequence: ggcagcgacatcagcaattcctattggtgcgcatattgtcagcaaggtacaaacgctgttGgcaagccagagtaaccccgg
                        -35                -10              +1                   
Evidence: [HIPP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [6] Schneider BL., et al., 2002
TF binding sites (TFBSs)
[Nac,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Nac activator gabDp1 2791121 2791135 -44.0 cggcagcgacATCAGCAATTCCTATtggtgcgcat nd [GEA], [HIBSCS] [6], [7]


Evidence    

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [HIPP] Human inference of promoter position

 [HIBSCS] Human inference based on similarity to consensus sequences


Reference(s)    

 [1] Metzner M., Germer J., Hengge R., 2004, Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli., Mol Microbiol 51(3):799-811

 [2] Marschall C., Labrousse V., Kreimer M., Weichart D., Kolb A., Hengge-Aronis R., 1998, Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP., J Mol Biol 276(2):339-53

 [3] Germer J., Becker G., Metzner M., Hengge-Aronis R., 2001, Role of activator site position and a distal UP-element half-site for sigma factor selectivity at a CRP/H-NS-activated sigma(s)-dependent promoter in Escherichia coli., Mol Microbiol 41(3):705-16

 [4] Knorr S., Sinn M., Galetskiy D., Williams RM., Wang C., Muller N., Mayans O., Schleheck D., Hartig JS., 2018, Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate., Nat Commun 9(1):5071

 [5] Traxler MF., Summers SM., Nguyen HT., Zacharia VM., Hightower GA., Smith JT., Conway T., 2008, The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli., Mol Microbiol 68(5):1128-48

 [6] Schneider BL., Ruback S., Kiupakis AK., Kasbarian H., Pybus C., Reitzer L., 2002, The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction., J Bacteriol 184(24):6976-86

 [7] Zimmer DP., Soupene E., Lee HL., Wendisch VF., Khodursky AB., Peter BJ., Bender RA., Kustu S., 2000, Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation., Proc Natl Acad Sci U S A 97(26):14674-9

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