RegulonDB RegulonDB 10.6.3: 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) |CITS:[2448295], [1447980]|.
The operon is the target of Lrp (global modulator in response to leucine levels, related to nitrogen metabolism) |CITS:[9236118], [3326786]|, IHF (global DNA-bending protein), and GadE (regulator for resistance to low pH) |CITS:[14702398]| activation, and Nac (regulator for the histidine and nitrogen utilization) |CITS:[11121068]|, and Fnr (global regulator in response to respiration changes) |CITS:[16377617]| repression. 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 |CITS:[11395454]|.
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 |CITS:[11395454]|.
A new site for Lrp controlling positively the gltBp promoter has been identified |CITS:[18405378]|. However, it was not considered, since it is 42 bp downstream from the transcriptional start site of gltB |CITS:[18405378]|.
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 |CITS:[21272324]|.
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: Sigma38, Sigma70
Distance from start of the gene: 216
Sequence: acatttctgtaccaataagcttgccatttgacctgtatcagctttcccgataagttggaaAtccgctggaagctttctgga
                            -35                    -10      +1                   
Evidence: [HIPP]
[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 gltBp nd nd nd nd nd [BPP] [16]
[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 [BPP], [GEA], [HIBSCS] [4], [8]
remote ArgR-L-arginine repressor gltBp 3354169 3354186 -331.5 aatcaaaattACCGAAATTTCATGCATAatcacataaa nd [BPP], [GEA], [HIBSCS] [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-cAMP repressor gltBp 3354433 3354454 -65.5 tttaataaagAATTTTGCGCTAAAGCACATTTctgtaccaat nd [BPP], [GEA], [HIBSCS], [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 [AIBSCS], [GEA] [14], [15]
[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] [15]
[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 [BPP], , [GEA], [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] [16]
[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 [BPP], [GEA] [4], [13]
proximal IHF activator gltBp 3354418 3354430 -85.0 ttttaatttcAGTCATTTAATAAagaattttgc nd [BPP], [GEA] [4], [13]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 activator gltBp 3354256 3354270 -246.0 aggcaaaaacAGTAGCATGAAACGTcattaccaat nd [BPP], [HIBSCS], [SM] [4], [10], [11]
remote Lrp2 activator gltBp 3354287 3354301 -215.0 caattaaggcAGTATAAAATGCTGGttttgtcgtc nd [BPP], [HIBSCS], [SM] [4], [5], [11]
remote Lrp3 activator gltBp 3354350 3354364 -152.0 cctttatgacAGTCAGGAATTGACTgtttctctaa nd [BPP], [HIBSCS], [SM] [4], [5], [11]
remote Lrp-leucine activator gltBp 3354394 3354409 -108.0 ttttagccttAAAGATAAAATCCATTttaatttcag nd [AIBSCS], [GEA] [12]
[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] [17]
Note(s): 1Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)
2Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)
3Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)
4Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)
5Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)
6Lrp activates the gltBDF operon in a leucine-insensitive manner Ernsting BR,1993 binding at three sites distant to the σ70 promoter. This is a strange way of regulating a σ70 promoter, since Lrp should bind close to the promoter in order to regulate, and so it is helped by IHF (the DNA-bending protein) binding between the proximal Lrp site and the promoter, bending this DNA region and getting Lrp closer to σ70 to activate the transcription Paul L,2001 (Lrp is just a modulator of the operon expression; it does not work as the common activators/repressors that switch the gene expression in an on/off manner. In addition, it is sometimes insensitive to the presence of leucine to have its modulator effect Calvo JM,1994)


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


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] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol 174(4):1109-18

 [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] 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

 [13] 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

 [14] 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

 [15] 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

 [16] 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

 [17] 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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