RegulonDB RegulonDB 10.10: 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 Metzner M,2004, 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) Knorr S,2018
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: [ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] 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-cyclic-AMP activator csiDp 2788848 2788869 -68.5 atgttactaaTTTGTTGCTTTTGATCACAATAagaaaacaat nd [GEA], [AIBSCS], [BPP] [3], [4]
[GlaR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal GlaR repressor csiDp 2788889 2788902 -32.0 tatgtcgcttTTGTGCGCATTTTTcagaaatgta nd [GEA], [IEP], [BPP] [1], [5]
proximal GlaR repressor csiDp 2788908 2788921 -13.0 tttttcagaaATGTAGATATTTTTagattatggc nd [GEA], [IEP], [RSE], [AIBSPD], [BPP], [CSE] [1], [5], [6]
[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-NS activator csiDp nd nd nd nd nd [GEA], [BPP] [4]
[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-L-leucine activator csiDp nd nd nd nd nd [GEA], [BPP] [3]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation csiDp nd   [EME] [7]
Evidence: [EME] Expression microarray evidence
Reference(s): [7] 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 Schneider BL,2002 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, Metzner M,2004 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 Knorr S,2018
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]
[ICWHO]
[IEP]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[8] Maciag A., et al., 2011
[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 Schneider BL,2002 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, Metzner M,2004 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 Knorr S,2018
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Metzner M., et al., 2004
[9] Schneider BL., et al., 2002
Promoter
Name: gabDp1
+1: 2791172
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 101
Sequence: ggcagcgacatcagcaattcctattggtgcgcatattgtcagcaaggtacaaacgctgttGgcaagccagagtaaccccgg
                        -35                     -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IEP]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[8] Maciag A., et al., 2011
[9] 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], [RSE], [AIBSPD], [APIORCISFBSCS], [CSE] [6], [9], [10]


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 Schneider BL,2002 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, Metzner M,2004 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 Knorr S,2018
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Metzner M., et al., 2004
[9] Schneider BL., et al., 2002
Promoter
Name: gabDp
+1: 2791172
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 101
Sequence: ggcagcgacatcagcaattcctattggtgcgcatattgtcagcaaggtacaaacgctgttGgcaagccagagtaaccccgg
                        -35                -10              +1                   
Evidence: [HIPP]
[ICWHO]
[IEP]
[IHBCE]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[8] Maciag A., et al., 2011
[9] 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 gabDp 2791121 2791135 -44.0 cggcagcgacATCAGCAATTCCTATtggtgcgcat nd [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [CSE] [6], [9], [10]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [IEP] Inferred from expression pattern

 [RSE] RNA-seq evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CSE] ChIP-seq evidence

 [HIPP] Human inference of promoter position

 [IHBCE] Inferred by a human based on computational evidence

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


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] 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] 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

 [4] 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

 [5] 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

 [6] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [7] 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

 [8] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [9] 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

 [10] 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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