Page last updated: 2024-10-24

nitrogen catabolite activation of transcription from RNA polymerase II promoter

Definition

Target type: biologicalprocess

A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources. [GOC:mah, GOC:txnOH, PMID:19104072]

Nitrogen catabolite repression (NCR) is a regulatory mechanism that allows bacteria to prioritize the utilization of preferred carbon sources, such as glucose, over less favorable ones. This process is mediated by the cyclic AMP receptor protein (CRP) and its co-factor, cyclic AMP (cAMP), which together form a complex that acts as a transcription activator.

When glucose is present, the intracellular concentration of cAMP is low, and CRP is inactive. As glucose is depleted, the cAMP concentration increases, leading to the formation of the active CRP-cAMP complex. This complex binds to specific DNA sequences called CRP-binding sites, which are located upstream of the promoters of many genes involved in the utilization of alternative carbon sources.

The binding of CRP-cAMP to these sites enhances the recruitment of RNA polymerase II (RNAP II) to the promoter, resulting in increased transcription of the corresponding genes.

In summary, the biological process of nitrogen catabolite activation of transcription from an RNA polymerase II promoter involves the following steps:

1. Glucose depletion leads to an increase in cAMP levels.
2. cAMP binds to CRP, activating it.
3. The CRP-cAMP complex binds to CRP-binding sites upstream of target gene promoters.
4. CRP-cAMP facilitates the recruitment of RNAP II to the promoter, promoting transcription.

This process ensures that the expression of genes encoding enzymes for the utilization of alternative carbon sources is only activated when glucose is scarce, allowing bacteria to optimize their metabolism.'
"

Proteins (1)

ProteinDefinitionTaxonomy
Bile acid receptorA bile acid receptor that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96RI1]Homo sapiens (human)

Compounds (44)

CompoundDefinitionClassesRoles
benzbromaronebenzbromarone : 1-Benzofuran substituted at C-2 and C-3 by an ethyl group and a 3,5-dibromo-4-hydroxybenzoyl group respectively. An inhibitor of CYP2C9, it is used as an anti-gout medication.

Benzbromarone: Uricosuric that acts by increasing uric acid clearance. It is used in the treatment of gout.
1-benzofurans;
aromatic ketone
uricosuric drug
clotrimazoleconazole antifungal drug;
imidazole antifungal drug;
imidazoles;
monochlorobenzenes
antiinfective agent;
environmental contaminant;
xenobiotic
felodipinefelodipine : The mixed (methyl, ethyl) diester of 4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic acid. A calcium-channel blocker, it lowers blood pressure by reducing peripheral vascular resistance through a highly selective action on smooth muscle in arteriolar resistance vessels. It is used in the management of hypertension and angina pectoris.

Felodipine: A dihydropyridine calcium antagonist with positive inotropic effects. It lowers blood pressure by reducing peripheral vascular resistance through a highly selective action on smooth muscle in arteriolar resistance vessels.
dichlorobenzene;
dihydropyridine;
ethyl ester;
methyl ester
anti-arrhythmia drug;
antihypertensive agent;
calcium channel blocker;
vasodilator agent
flutrimazoleflutrimazole : An imidazole antifungal agent that is imidazole in which the hydrogen attached to the nitrogen is replaced by a 2,4'-difluorotrityl group. A topical antifungal agent which displays potent broad-spectrum in vitro activity against dermatophytes, filamentous fungi and yeasts.imidazole antifungal drug;
imidazoles;
monofluorobenzenes
EC 1.14.13.70 (sterol 14alpha-demethylase) inhibitor
loratadineloratadine : A benzocycloheptapyridine that is 6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridine substituted by a chloro group at position 8 and a 1-(ethoxycarbonyl)piperidin-4-ylidene group at position 11. It is a H1-receptor antagonist commonly employed in the treatment of allergic disorders.

Loratadine: A second-generation histamine H1 receptor antagonist used in the treatment of allergic rhinitis and urticaria. Unlike most classical antihistamines (HISTAMINE H1 ANTAGONISTS) it lacks central nervous system depressing effects such as drowsiness.
benzocycloheptapyridine;
ethyl ester;
N-acylpiperidine;
organochlorine compound;
tertiary carboxamide
anti-allergic agent;
cholinergic antagonist;
geroprotector;
H1-receptor antagonist
nimodipinenimodipine : A dihydropyridine that is 1,4-dihydropyridine which is substituted by methyl groups at positions 2 and 6, a (2-methoxyethoxy)carbonyl group at position 3, a m-nitrophenyl group at position 4, and an isopropoxycarbonyl group at position 5. An L-type calcium channel blocker, it acts particularly on cerebral circulation, and is used both orally and intravenously for the prevention and treatment of subarachnoid hemorrhage from ruptured intracranial aneurysm.

Nimodipine: A calcium channel blockader with preferential cerebrovascular activity. It has marked cerebrovascular dilating effects and lowers blood pressure.
2-methoxyethyl ester;
C-nitro compound;
dicarboxylic acids and O-substituted derivatives;
diester;
dihydropyridine;
isopropyl ester
antihypertensive agent;
calcium channel blocker;
cardiovascular drug;
vasodilator agent
ono 1078pranlukast: SRS-A antagonist; leukotriene D4 receptor antagonistchromones
raloxifeneraloxifene : A member of the class of 1-benzothiophenes that is 1-benzothiophene in which the hydrogens at positions 2, 3, and 6 have been replaced by p-hydroxyphenyl, p-[2-(piperidin-1-yl)ethoxy]benzoyl, and hydroxy groups, respectively.1-benzothiophenes;
aromatic ketone;
N-oxyethylpiperidine;
phenols
bone density conservation agent;
estrogen antagonist;
estrogen receptor modulator
sulconazole1-{2-[(4-chlorobenzyl)sulfanyl]-2-(2,4-dichlorophenyl)ethyl}-1H-imidazole : A member of the class of imidazoles that is 1-ethyl-1H-imidazole in which one of the hydrogens of the methyl group is replaced by a (4-chlorobenzyl)sulfanediyl group while a second is replaced by a 2,4-dichlorophenyl group.

sulconazole : A racemate comprising equimolar amounts of (R)- and (S)-sulconazole. An antifungal agent with activity against Candida species, it is used (generally as the nitrate salt) for the topical treatment of fungal skin infections.

sulconazole: RN given refers to cpd with unspecified isomeric designation; structure given in first source
dichlorobenzene;
imidazoles;
monochlorobenzenes;
organic sulfide
thyroxinethyroxine : An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions.

Thyroxine: The major hormone derived from the thyroid gland. Thyroxine is synthesized via the iodination of tyrosines (MONOIODOTYROSINE) and the coupling of iodotyrosines (DIIODOTYROSINE) in the THYROGLOBULIN. Thyroxine is released from thyroglobulin by proteolysis and secreted into the blood. Thyroxine is peripherally deiodinated to form TRIIODOTHYRONINE which exerts a broad spectrum of stimulatory effects on cell metabolism.
2-halophenol;
iodophenol;
L-phenylalanine derivative;
non-proteinogenic L-alpha-amino acid;
thyroxine;
thyroxine zwitterion
antithyroid drug;
human metabolite;
mouse metabolite;
thyroid hormone
lithocholic acidlithocholate : A bile acid anion that is the conjugate base of lithocholic acid.

lithocholic acid : A monohydroxy-5beta-cholanic acid with a alpha-hydroxy substituent at position 3. It is a bile acid obtained from chenodeoxycholic acid by bacterial action.

Lithocholic Acid: A bile acid formed from chenodeoxycholate by bacterial action, usually conjugated with glycine or taurine. It acts as a detergent to solubilize fats for absorption and is itself absorbed. It is used as cholagogue and choleretic.
bile acid;
C24-steroid;
monohydroxy-5beta-cholanic acid
geroprotector;
human metabolite;
mouse metabolite
chenodeoxycholic acidchenodeoxycholate : Conjugate base of chenodeoxycholic acid; major species at pH 7.3.

chenodeoxycholic acid : A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively.

Chenodeoxycholic Acid: A bile acid, usually conjugated with either glycine or taurine. It acts as a detergent to solubilize fats for intestinal absorption and is reabsorbed by the small intestine. It is used as cholagogue, a choleretic laxative, and to prevent or dissolve gallstones.
bile acid;
C24-steroid;
dihydroxy-5beta-cholanic acid
human metabolite;
mouse metabolite
glycochenodeoxycholic acidglycochenodeoxycholate : A N-acylglycinate that is the conjugate base of glycochenodeoxycholic acid.

glycochenodeoxycholic acid : A bile acid glycine conjugate having 3alpha,7alpha-dihydroxy-5beta-cholan-24-oyl as the bile acid component.

Glycochenodeoxycholic Acid: A bile salt formed in the liver from chenodeoxycholate and glycine, usually as the sodium salt. It acts as a detergent to solubilize fats for absorption and is itself absorbed. It is a cholagogue and choleretic.
bile acid glycine conjugatehuman metabolite
ursodeoxycholic acidursodeoxycholate : A bile acid anion that is the conjugate base of ursodeoxycholic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3.

ursodeoxycholic acid : A bile acid found in the bile of bears (Ursidae) as a conjugate with taurine. Used therapeutically, it prevents the synthesis and absorption of cholesterol and can lead to the dissolution of gallstones.

Ursodeoxycholic Acid: An epimer of chenodeoxycholic acid. It is a mammalian bile acid found first in the bear and is apparently either a precursor or a product of chenodeoxycholate. Its administration changes the composition of bile and may dissolve gallstones. It is used as a cholagogue and choleretic.
bile acid;
C24-steroid;
dihydroxy-5beta-cholanic acid
human metabolite;
mouse metabolite
fulvestrantfulvestrant : A 3-hydroxy steroid that is 17beta-estradiol in which the 7alpha hydrogen has been replaced by a nonyl group in which one of the hydrogens of the terminal methyl has been replaced by a (4,4,5,5,5-pentafluoropentyl)sulfinyl group. An estrogen receptor antagonist, it is used in the treatment of breast cancer.

Fulvestrant: An estradiol derivative and estrogen receptor antagonist that is used for the treatment of estrogen receptor-positive, locally advanced or metastatic breast cancer.
17beta-hydroxy steroid;
3-hydroxy steroid;
organofluorine compound;
sulfoxide
antineoplastic agent;
estrogen antagonist;
estrogen receptor antagonist
6-hydroxydopa6-hydroxydopa: RN given refers to cpd without isomeric designationnon-proteinogenic alpha-amino acid
ly 255283LY 255283: structure given in UD; leukotriene B4 antagonistaromatic ketone
nbi 27914dialkylarylamine;
tertiary amino compound
cholic acidcholic acid : A bile acid that is 5beta-cholan-24-oic acid bearing three alpha-hydroxy substituents at position 3, 7 and 12.

Cholic Acid: A major primary bile acid produced in the liver and usually conjugated with glycine or taurine. It facilitates fat absorption and cholesterol excretion.
12alpha-hydroxy steroid;
3alpha-hydroxy steroid;
7alpha-hydroxy steroid;
bile acid;
C24-steroid;
trihydroxy-5beta-cholanic acid
human metabolite;
mouse metabolite
deoxycholic aciddeoxycholic acid : A bile acid that is 5beta-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 12 respectively.

Deoxycholic Acid: A bile acid formed by bacterial action from cholate. It is usually conjugated with glycine or taurine. Deoxycholic acid acts as a detergent to solubilize fats for intestinal absorption, is reabsorbed itself, and is used as a choleretic and detergent.
bile acid;
C24-steroid;
dihydroxy-5beta-cholanic acid
human blood serum metabolite
taurochenodeoxycholic acidtaurochenodeoxycholate : An organosulfonate oxoanion that is the conjugate base of taurochenodeoxycholic acid arising from deprotonation of the sulfonate OH group; major species at pH 7.3.

taurochenodeoxycholic acid : A bile acid taurine conjugate of chenodeoxycholic acid.

Taurochenodeoxycholic Acid: A bile salt formed in the liver by conjugation of chenodeoxycholate with taurine, usually as the sodium salt. It acts as detergent to solubilize fats in the small intestine and is itself absorbed. It is used as a cholagogue and choleretic.
bile acid taurine conjugatehuman metabolite;
mouse metabolite
5,11-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol(R,R)-5,11-diethyl-5,6,11,12-tetrahydro-2,8-chrysenediol : A carbotetracyclic compound that is 5,6,11,12-tetrahydrochrysene substituted by hydroxy groups at positions 2 and 8 and by ethyl groups at positions 5 and 11 (the 5R,11R-stereoisomer). It is an agonist of ER-alpha and antagonist of ER-beta receptors.

5,11-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol: estrogen receptor ligand; structure in first source
carbotetracyclic compound;
polyphenol
estrogen receptor agonist;
estrogen receptor antagonist;
geroprotector;
neuroprotective agent
obeticholic acidobeticholic acid : A dihydroxy-5beta-cholanic acid that is chenodeoxycholic acid carrying an additional ethyl substituent at the 6alpha-position. A semi-synthetic bile acid which acts as a farnesoid X receptor agonist and is used for treatment of primary biliary cholangitis.

obeticholic acid: A farnesoid X receptor agonist and anticholestatic agent that is used in the treatment of chronic liver diseases; structure in first source.
3alpha-hydroxy steroid;
7alpha-hydroxy steroid;
dihydroxy-5beta-cholanic acid
farnesoid X receptor agonist;
hepatoprotective agent
t0901317T0901317: an LXRalpha and LXRbeta agonist
6-bromoindirubin-3'-oxime6-bromoindirubin-3'-oxime : A member of the class of biindoles that is indirubin substituted at position 6 by a bromo group and in which the keto group at position 3' has undergone condensation with hydroxylamine to form the corresponding oxime.

6-bromoindirubin-3'-oxime: structure in first source
gw 7647GW 7647 : A monocarboxylic acid that is 2-(phenylsulfanyl)isobutyric acid in which the phenyl group is substituted at the para- position by a 3-aza-7-cyclohexylhept-1-yl group in which the nitrogen is acylated by a (cyclohexylamino)carbonyl group.

GW 7647: a PPAR-alpha agonist; structure in first source
aryl sulfide;
monocarboxylic acid;
ureas
PPARalpha agonist
jhw 015indolecarboxamide
andrographolidecarbobicyclic compound;
gamma-lactone;
labdane diterpenoid;
primary alcohol;
secondary alcohol
anti-HIV agent;
anti-inflammatory drug;
antineoplastic agent;
metabolite
fexaraminefexaramine: structure in first sourcebiphenyls
pregna-4,17-diene-3,16-dionepregna-4,17-diene-3,16-dione: steroid from guggulu extract; RN & N1 from C1 Form index; RN given refers to cpd without isomeric designation; structure in first source; antagonist of farnesoid X receptor3-hydroxy steroidandrogen
pregna-4,17-diene-3,16-dione, (17z)-isomer
gw 4064stilbenoid
way-362450indoles
12-epi-scalarin12-epi-scalarin : The 12-epimer of scalarin, a metabolite of marine sponges of the genus Spongia.scalarane sesterterpenoidanimal metabolite
glycoursodeoxycholic acidglycoursodeoxycholate : A N-acylglycinate that is the conjugate base of glycoursodeoxycholic acid. obtained by deprotonation of the carboxy group; major species at pH 7.3.

glycoursodeoxycholic acid : A bile acid glycine conjugate derived from ursoodeoxycholic acid.
bile acid glycine conjugate;
N-acylglycine
human blood serum metabolite;
neuroprotective agent
alisol b monoacetatealisol B 23-acetate: from Alisma orientale rhizome; structure in first sourcetriterpenoid
alisol c 23-acetatealisol C 23-acetate: isolated from Alismatis Rhizoma; structure in first source
alisol aalisol A: has anti-hepatitis B virus activity; structure
alisol btriterpenoid
archazolid aarchazolid A: inhibits vacuolar-type ATPase; isolated from Archangium gephyra; structure in first source
int-777
alisol f
alisol a 24-acetatealisol A 24-acetate: isolated from Alismatis Rhizoma; structure in first source
4-(2-(2-chloro-4-((5-cyclopropyl-3-(2,6-dichlorophenyl)-4-isoxazolyl)methoxy)phenyl)cyclopropyl)benzoic acid4-(2-(2-chloro-4-((5-cyclopropyl-3-(2,6-dichlorophenyl)-4-isoxazolyl)methoxy)phenyl)cyclopropyl)benzoic acid: a farnesoid X receptor agonist; structure in first source