RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: guaBA
Synonym(s): OP00288
Gene(s): guaA, guaB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on genome-wide analysis, 472 single-gene knockouts were studied to determine their anaerobic fermentation products, based on the control of redox reactions. It was determined that the combined knockout of the guaB, pyrD, serA, fnr, arcA, and arcB genes enhanced D-lactate overproduction Kim HJ,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IMP-POLAR-MUTATION] Polar mutation
[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s): [1] Hutchings MI., et al., 2000
[2] Lambden PR., et al., 1973
[3] Shimada K., et al., 1976
[4] Tesfa-Selase F., et al., 1992
[5] Vales LD., et al., 1979
Promoter
Name: guaBp
+1: 2634107
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: agcaagcattttttgcaaaaaggggtagatgcaatcggttacgctctgtataatgccgcgGcaatatttattaaccactct
                              -35                     -10   +1                   
Note(s): The Escherichia coli guaB promoter (PguaB) regulates transcription of the guaBA operon, encoding GuaB and GuaA, which are required for the de novo synthesis of GMP.
Between the guaB and guaA genes exists a 68-bp intercistronic region that contains a palindromic sequence and could form a possible ρ-independent terminator, but the effect of this possible hairpin loop should be modest over the expression of the guaB gene Tiedeman AA,1985
In 1977, Fukumaki et al. showed that the transcription of the guaA gene can be dependent on a secondary promoter located within the guaB gene, but the precise position was not located Fukumaki Y, Shimada K, Takagi Y,1977 Evidence to demonstrate this was obtained by using a fago lambda-pguaA transducing phage Fukumaki Y, Shimada K, Takagi Y,1977
The activity of guaBp is subject to growth rate-dependent control (GRDC), that is, the activity of guaBp increases as a function of the cellular growth rate Davies IJ,1996. Husnain SI, Thomas MS,2008. Husnain SI,2008 Two elements are required for this regulation, an UP element, located between -59 and -38 relative to the guaB transcriptional start site Husnain SI, Thomas MS,2008 and a binding site for cAMP-CRP, located over 100 bp upstream of the transcription start site. cAMP-CRP, bound to this upstream site, downregulates guaBp. Downregulation is influenced by the growth rate and not by the carbon source Husnain SI,2009 The UP element, which is also required for GRDC, contains two independent subsites that are able to activate transcription independently. It stimulates guaBA transcription ~8- to 10-fold both in vivo and in vitro, and this activity requires the C-terminal domain of the RNA polymerase α-subunit Husnain SI, Thomas MS,2008 The mechanism by which cAMP-CRP together with the UP element regulate transcription in a growth rate-dependent manner is not yet clear.
Based on deletion analysis, purified proteins of FIS, and multiple in vitro transcription assays, Husnain and Thomas (2008) Husnain SI,2008proved that the putative FIS-binding sites (-126, -109, -92, and -76) located upstream of the guaBp core elements are not functional, since FIS does not bind in these sites, and they were removed from EcoCyc. Binding of FIS to sites FIS I, II, and III (-11, +8, and +29, respectively), identified by Husnain and Thomas (2008), represses transcription from guaBA ~8- to 10-fold in vitro but not in vivo Husnain SI,2008
guaBp is repressed by PurR, and the binding site for PurR overlaps the core promoter Husnain SI,2009. Davies IJ,1996 Expression of guaB is also repressed by DnaA in vivo. A consensus binding site, located approximately 200 bp downstream from the translation initiation codon, is required for DnaA-mediated repression at guaBp Tesfa-Selase F,1996. Tesfa-Selase F,1992 The role of a second, nonconsensus DnaA site overlapping the guaB promoter is not yet clear. In addition, guaBp carries a GC-rich discriminator Andrews SC, Guest JR,1988
Neither Fis nor DnaA or PurR is required for GRDC of guaBp Husnain SI,2008. Husnain SI,2009
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Davies IJ., et al., 1996
[7] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: ttgaagataaAAAACCCTCTGTAGTAACAGAGGGTTTTgttcattcat
Reference(s): [8] Tiedeman AA., et al., 1985
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator guaBp 2634214 2634235 -117.5 tgagaaggtaACATGTGAGCGAGATCAAATTCtaaatcagca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
[DnaA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote DnaA-ATP repressor guaBp 2633856 2633864 248.0 gtatcggcttTATCCACAAaaacatgtcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [13]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor guaBp 2634072 2634086 29.0 taaccactctGGTCGAGATATTGCCcatgctacgt nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [12]
proximal Fis repressor guaBp 2634093 2634107 8.0 taatgccgcgGCAATATTTATTAACcactctggtc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [12]
proximal Fis repressor guaBp 2634111 2634125 -11.0 aatcggttacGCTCTGTATAATGCCgcggcaatat nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [12]
[PurR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PurR-hypoxanthine repressor guaBp 2634124 2634139 -24.5 aaaggggtagATGCAATCGGTTACGCtctgtataat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [10], [11]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.5 2634072 2634108 ataatgccgcGGCAATATTTATTAACCACTCTGGTCGAGATATTGCccatgctacg
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Hutchings MI., Drabble WT., 2000, Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein., FEMS Microbiol Lett 187(2):115-22

 [2] Lambden PR., Drabble WT., 1973, The gua operon of Escherichia coli K-12: evidence for polarity from guaB to guaA., J Bacteriol 115(3):992-1002

 [3] Shimada K., Fukumaki Y., Takagi Y., 1976, Expression of the guanine operon of Escherichia coli as analyzed by bacteriophage lambda induced mutations., Mol Gen Genet 147(2):203-8

 [4] Tesfa-Selase F., Drabble WT., 1992, Regulation of the gua operon of Escherichia coli by the DnaA protein., Mol Gen Genet 231(2):256-64

 [5] Vales LD., Chase JW., Murphy JB., 1979, Orientation of the guanine operon of Escherichia coli K-12 by utilizing strains containing guaB-xse and guaB-upp deletions., J Bacteriol 139(1):320-2

 [6] Davies IJ., Drabble WT., 1996, Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12., Microbiology 142 ( Pt 9):2429-37

 [7] 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

 [8] Tiedeman AA., Smith JM., Zalkin H., 1985, Nucleotide sequence of the guaA gene encoding GMP synthetase of Escherichia coli K12., J Biol Chem 260(15):8676-9

 [9] Husnain SI., Busby SJ., Thomas MS., 2009, Downregulation of the Escherichia coli guaB promoter by upstream-bound cyclic AMP receptor protein., J Bacteriol 191(19):6094-104

 [10] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res 39(15):6456-64

 [11] Meng LM., Kilstrup M., Nygaard P., 1990, Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli., Eur J Biochem 187(2):373-9

 [12] Husnain SI., Thomas MS., 2008, Downregulation of the Escherichia coli guaB promoter by FIS., Microbiology 154(Pt 6):1729-38

 [13] Tesfa-Selase F., Drabble WT., 1996, Specific binding of DnaA protein to a DnaA box in the guaB gene of Escherichia coli K12., Eur J Biochem 241(2):411-6

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