RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: katG
Synonym(s): OP00043
Gene(s): katG   Genome Browser M3D Gene expression COLOMBOS
Note(s): Jung IL,2003demonstrated that both oxyR and katG gene expression, which codify a transcriptional regulator and a product essential for the detoxification against H2O2-induced stress, respectively, were absolutely dependent on polyamines during entry into the stationary phase. These data suggest that polyamines could be directly participating in the defense mechanism against oxidative stress. Both putrecine and spermidine polyamines increase expression of of the oxyR and katG genes, which are responsible for defense against oxidative stress Tkachenko AG, Nesterova LY,2003.
The transcription of the gene katG is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
It was found that 1.4-W/cm2 130-μm terahertz (THz) radiation activated the promoters of genes related to oxidative stress and copper ion homeostasis through katG and copA genes Demidova EV, Goryachkovskaya TN, Malup TK, Bannikova SV, Semenov AI, Vinokurov NA, Kolchanov NA, Popik VM, Peltek SE,2013
Sulfane sulfur modifies OxyR at Cys199 to form a protein persulfide that in turn activates the expression of grxA, trxC, and katG promoters under both aerobic and anaerobic conditions Hou N, Yan Z, Fan K, Li H, Zhao R, Xia Y, Xun L, Liu H,2019
The transcript of katG is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for katG . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Demidova EV, Goryachkovskaya TN, Malup TK, Bannikova SV, Semenov AI, Vinokurov NA, Kolchanov NA, Popik VM, Peltek SE,2013
Reference(s): [1] Gonzalez-Flecha B., et al., 1997
Promoter
Name: katGp
+1: 4133812
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 23
Sequence: atcgcatccgtggattaattcaattataacttctctctaacgctgtgtatcgtaacggtaAcactgtagaggggagcacat
                        -35                     -10         +1                   
Note(s): Rpos has been shown to control the transcription of the katG gene. Ivanova A, Miller C, Glinsky G, Eisenstark A,1994| found that expression of the katG gene was significantly diminished after the inactivation of the rpoS gene, principally in stationary phase. Nitric oxide (NO) reduces the hydrogen peroxide (H2O2)-induced protein output from the katGp promoter Adolfsen KJ, Chou WK, Brynildsen MP,2019
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Tartaglia LA., et al., 1989
[4] Triggs-Raine BL., et al., 1988
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator katGp 4133693 4133706 -112.5 atcaaaaaagCTTAATTAAGATCAatttgatcta nd [GEA], [AIBSCS] [6]
remote FNR activator katGp 4133709 4133722 -96.5 taagatcaatTTGATCTACATCTCtttaaccaac nd [EME], [GEA], [AIBSCS], [AIBSPD], [CCE] [6], [7]
[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+ activator katGp nd nd nd nd nd [IEP], [BPP] [13]
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR activator katGp 4133738 4133754 -66.0 ccaacaatatGTAAGATCTCAACTATCgcatccgtgg [GEA], [RSE], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] [3], [8], [9], [10], [11], [12]
proximal OxyR activator katGp 4133760 4133776 -44.0 ctatcgcatcCGTGGATTAATTCAATTataacttctc [GEA], [APIORCISFBSCS], [BPP] [3], [9], [10], [11], [12]
proximal OxyR activator katGp 4133805 4133821 2.0 tgtgtatcgtAACGGTAACACTGTAGAggggagcaca nd [RSE], [CEEUMA], [IHBCE] [8]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA SdhX katG repressor 4133815 4133828 CUGUAGAGGGGAGC nd [IEP], [SM] [5]


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [EME] Expression microarray evidence

 [AIBSPD] Automated inference based on sequence pattern discovery

 [CCE] ChIP-chip evidence

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [RSE] RNA-seq evidence

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

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [SM] Site mutation


Reference(s)    

 [1] Gonzalez-Flecha B., Demple B., 1997, Homeostatic regulation of intracellular hydrogen peroxide concentration in aerobically growing Escherichia coli., J Bacteriol 179(2):382-8

 [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] Tartaglia LA., Storz G., Ames BN., 1989, Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress., J Mol Biol 210(4):709-19

 [4] Triggs-Raine BL., Doble BW., Mulvey MR., Sorby PA., Loewen PC., 1988, Nucleotide sequence of katG, encoding catalase HPI of Escherichia coli., J Bacteriol 170(9):4415-9

 [5] Miyakoshi M., Matera G., Maki K., Sone Y., Vogel J., 2019, Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA., Nucleic Acids Res 47(4):2075-2088

 [6] 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

 [7] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [8] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [9] Storz G., Tartaglia LA., Ames BN., 1990, Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation., Science 248(4952):189-94

 [10] Tartaglia LA., Gimeno CJ., Storz G., Ames BN., 1992, Multidegenerate DNA recognition by the OxyR transcriptional regulator., J Biol Chem 267(3):2038-45

 [11] Toledano MB., Kullik I., Trinh F., Baird PT., Schneider TD., Storz G., 1994, Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection., Cell 78(5):897-909

 [12] Zheng M., Wang X., Doan B., Lewis KA., Schneider TD., Storz G., 2001, Computation-directed identification of OxyR DNA binding sites in Escherichia coli., J Bacteriol 183(15):4571-9

 [13] Hoerter JD., Arnold AA., Ward CS., Sauer M., Johnson S., Fleming T., Eisenstark A., 2005, Reduced hydroperoxidase (HPI and HPII) activity in the Deltafur mutant contributes to increased sensitivity to UVA radiation in Escherichia coli., J Photochem Photobiol B 79(2):151-7

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