RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: gltBDF
Synonym(s): OP00253, gltD
Gene(s): gltB, gltD, gltF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The gltBDF operon codes for the glutamate synthase, the large (gltB) and small (gltD) subunits, and a protein that is implied in the self-operon regulation (gltF) Castano I,1988. Castano I,1992
The operon is the target of Lrp (global modulator in response to leucine levels, related to nitrogen metabolism) Wiese DE,1997. Oliver G,1987 IHF (global DNA-bending protein), and GadE (regulator for resistance to low pH) Hommais F,2004activation, and Nac (regulator for the histidine and nitrogen utilization) Zimmer DP,2000 and Fnr (global regulator in response to respiration changes) Constantinidou C,2006repression. The Lrp activation is helped by the IHF binding between the promoter and its proximal Lrp site (the one centered at ?152 bp), by which Lrp gets closer to the σ70 to activate Paul L,2001
An important detail about the proximal Lrp and IHF sites is that the same order and approximate distances and sequences of the sites and the promoter are conserved among several related organisms of the Enterobacteriaceae genera Paul L,2001
A new site for Lrp controlling positively the gltBp promoter has been identified Lintner RE,2008 However, it was not considered, since it is 42 bp downstream from the transcriptional start site of gltB Lintner RE,2008
Under nitrogen-rich growth conditions, the expression of this operon was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Castano I., et al., 1988
[2] Castano I., et al., 1992
[3] Grassl G., et al., 1999
[4] Paul L., et al., 2007
Promoter
Name: gltBp2
+1: 3354509
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 216
Sequence: acatttctgtaccaataagcttgccatttgacctgtatcagctttcccgataagttggaaAtccgctggaagctttctgga
Evidence: [HIPP]
[IPI]
[TIM]
Reference(s): [5] Oliver G., et al., 1987
[6] Seo SW., et al., 2015
[7] Velazquez L., et al., 1991
TF binding sites (TFBSs)
[AdiY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd AdiY activator gltBp2 nd nd nd nd nd [BPP] [17]
[ArgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArgR-L-arginine repressor gltBp2 3354148 3354165 -352.0 gcttttatcaACTGCATAATCAATCAAAattaccgaaa nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
remote ArgR-L-arginine repressor gltBp2 3354169 3354186 -331.5 aatcaaaattACCGAAATTTCATGCATAatcacataaa nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
[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 repressor gltBp2 3354433 3354454 -65.5 tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat nd [GEA], [APIORCISFBSCS], [BPP], [SM] [4]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor gltBp2 3354476 3354489 -26.5 agcttgccatTTGACCTGTATCAGctttcccgat nd [GEA], [AIBSCS] [15], [16]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor gltBp2 nd nd nd nd nd [GEA], [BPP] [16]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadE activator gltBp2 3354215 3354234 -284.0 gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt nd [GEA], [RSE], [BPP], [CEEUMA], [IHBCE] [6], [9]
[HdfR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HdfR activator gltBp2 nd nd nd nd nd [BPP] [17]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator gltBp2 3354414 3354426 -89.0 tccattttaaTTTCAGTCATTTAataaagaatt nd [GEA], [BPP] [4], [14]
proximal IHF activator gltBp2 3354418 3354430 -85.0 ttttaatttcAGTCATTTAATAAagaattttgc nd [GEA], [BPP] [4], [14]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp activator gltBp2 3354256 3354270 -246.0 aggcaaaaacAGTAGCATGAAACGTcattaccaat nd [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [10], [11]
remote Lrp activator gltBp2 3354287 3354301 -215.0 caattaaggcAGTATAAAATGCTGGttttgtcgtc nd [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [10], [11], [12]
remote Lrp activator gltBp2 3354350 3354364 -152.0 cctttatgacAGTCAGGAATTGACTgtttctctaa nd [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [10], [11]
remote Lrp-L-leucine activator gltBp2 3354394 3354409 -108.0 ttttagccttAAAGATAAAATCCATTttaatttcag nd [GEA], [RSE], [AIBSCS], [CSE] [10], [13]
[Nac,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Nac repressor gltBp2 nd nd nd nd nd [GEA], [BPP] [18]


Transcription unit          
Name: gltBDF
Synonym(s): OP00253, gltD
Gene(s): gltB, gltD, gltF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The gltBDF operon codes for the glutamate synthase, the large (gltB) and small (gltD) subunits, and a protein that is implied in the self-operon regulation (gltF) Castano I,1988. Castano I,1992
The operon is the target of Lrp (global modulator in response to leucine levels, related to nitrogen metabolism) Wiese DE,1997. Oliver G,1987 IHF (global DNA-bending protein), and GadE (regulator for resistance to low pH) Hommais F,2004activation, and Nac (regulator for the histidine and nitrogen utilization) Zimmer DP,2000 and Fnr (global regulator in response to respiration changes) Constantinidou C,2006repression. The Lrp activation is helped by the IHF binding between the promoter and its proximal Lrp site (the one centered at ?152 bp), by which Lrp gets closer to the σ70 to activate Paul L,2001
An important detail about the proximal Lrp and IHF sites is that the same order and approximate distances and sequences of the sites and the promoter are conserved among several related organisms of the Enterobacteriaceae genera Paul L,2001
A new site for Lrp controlling positively the gltBp promoter has been identified Lintner RE,2008 However, it was not considered, since it is 42 bp downstream from the transcriptional start site of gltB Lintner RE,2008
Under nitrogen-rich growth conditions, the expression of this operon was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [1] Castano I., et al., 1988
[2] Castano I., et al., 1992
[3] Grassl G., et al., 1999
[4] Paul L., et al., 2007
Promoter
Name: gltBp
+1: 3354509
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 216
Sequence: acatttctgtaccaataagcttgccatttgacctgtatcagctttcccgataagttggaaAtccgctggaagctttctgga
                            -35                    -10      +1                   
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [19] Huerta AM., et al., 2003
[5] Oliver G., et al., 1987
[6] Seo SW., et al., 2015
[7] Velazquez L., et al., 1991
TF binding sites (TFBSs)
[AdiY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd AdiY activator gltBp nd nd nd nd nd [BPP] [17]
[ArgR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArgR-L-arginine repressor gltBp 3354148 3354165 -352.0 gcttttatcaACTGCATAATCAATCAAAattaccgaaa nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
remote ArgR-L-arginine repressor gltBp 3354169 3354186 -331.5 aatcaaaattACCGAAATTTCATGCATAatcacataaa nd [GEA], [APIORCISFBSCS], [BPP] [4], [8]
[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 repressor gltBp 3354433 3354454 -65.5 tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat nd [GEA], [APIORCISFBSCS], [BPP], [SM] [4]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor gltBp 3354476 3354489 -26.5 agcttgccatTTGACCTGTATCAGctttcccgat nd [GEA], [AIBSCS] [15], [16]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ repressor gltBp nd nd nd nd nd [GEA], [BPP] [16]
[GadE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GadE activator gltBp 3354215 3354234 -284.0 gcttatcttgTGTCAGATTTTTTTATCTCCtgatggattt nd [GEA], [RSE], [BPP], [CEEUMA], [IHBCE] [6], [9]
[HdfR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HdfR activator gltBp nd nd nd nd nd [BPP] [17]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator gltBp 3354414 3354426 -89.0 tccattttaaTTTCAGTCATTTAataaagaatt nd [GEA], [BPP] [4], [14]
proximal IHF activator gltBp 3354418 3354430 -85.0 ttttaatttcAGTCATTTAATAAagaattttgc nd [GEA], [BPP] [4], [14]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp activator gltBp 3354256 3354270 -246.0 aggcaaaaacAGTAGCATGAAACGTcattaccaat nd [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [10], [11]
remote Lrp activator gltBp 3354287 3354301 -215.0 caattaaggcAGTATAAAATGCTGGttttgtcgtc nd [EME], [RSE], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE], [CSE], [SM] [4], [5], [10], [11], [12]
remote Lrp activator gltBp 3354350 3354364 -152.0 cctttatgacAGTCAGGAATTGACTgtttctctaa nd [RSE], [APIORCISFBSCS], [BPP], [CSE], [SM] [4], [5], [10], [11]
remote Lrp-L-leucine activator gltBp 3354394 3354409 -108.0 ttttagccttAAAGATAAAATCCATTttaatttcag nd [GEA], [RSE], [AIBSCS], [CSE] [10], [13]
[Nac,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Nac repressor gltBp nd nd nd nd nd [GEA], [BPP] [18]


Transcription unit       
Name: gltF
Gene(s): gltF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [NTAS] Non-traceable author statement


Evidence    

 [HIPP] Human inference of promoter position

 [IPI] Inferred from physical interaction

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

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

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [RSE] RNA-seq evidence

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [CSE] ChIP-seq evidence

 [EME] Expression microarray evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CCE] ChIP-chip evidence

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Castano I., Bastarrachea F., Covarrubias AA., 1988, gltBDF operon of Escherichia coli., J Bacteriol 170(2):821-7

 [2] Castano I., Flores N., Valle F., Covarrubias AA., Bolivar F., 1992, gltF, a member of the gltBDF operon of Escherichia coli, is involved in nitrogen-regulated gene expression., Mol Microbiol 6(18):2733-41

 [3] Grassl G., Bufe B., Muller B., Rosel M., Kleiner D., 1999, Characterization of the gltF gene product of Escherichia coli., FEMS Microbiol Lett 179(1):79-84

 [4] Paul L., Mishra PK., Blumenthal RM., Matthews RG., 2007, Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR., BMC Microbiol 7:2

 [5] Oliver G., Gosset G., Sanchez-Pescador R., Lozoya E., Ku LM., Flores N., Becerril B., Valle F., Bolivar F., 1987, Determination of the nucleotide sequence for the glutamate synthase structural genes of Escherichia coli K-12., Gene 60(1):1-11

 [6] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [7] Velazquez L., Camarena L., Reyes JL., Bastarrachea F., 1991, Mutations affecting the Shine-Dalgarno sequences of the untranslated region of the Escherichia coli gltBDF operon., J Bacteriol 173(10):3261-4

 [8] Cho S., Cho YB., Kang TJ., Kim SC., Palsson B., Cho BK., 2015, The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli., Nucleic Acids Res 43(6):3079-88

 [9] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [10] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [11] Wiese DE., Ernsting BR., Blumenthal RM., Matthews RG., 1997, A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli., J Mol Biol 270(2):152-68

 [12] Cho BK., Barrett CL., Knight EM., Park YS., Palsson BO., 2008, Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli., Proc Natl Acad Sci U S A 105(49):19462-7

 [13] Lintner RE., Mishra PK., Srivastava P., Martinez-Vaz BM., Khodursky AB., Blumenthal RM., 2008, Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio., BMC Microbiol 8:60

 [14] Paul L., Blumenthal RM., Matthews RG., 2001, Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF., J Bacteriol 183(13):3910-8

 [15] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [16] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [17] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

 [18] 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

 [19] 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

RegulonDB