The L-arabinose operon of the model

Model organism

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...

 bacterium Escherichia coli

Escherichia coli

Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...

has been a focus for research in molecular biology

Molecular biology

Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...

 for over 40 years, and has been investigated extensively at the genetic

Genetics

Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....

, biochemical, physiological, and biophysical levels.
It is controlled by a dual positive and negative system.
There are 3 structural genes: araB, araA, and araD. They encode the metabolic enzymes for
breaking down the monosaccharide

Monosaccharide

Monosaccharides are the most basic units of biologically important carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose...

 sugar arabinose

Arabinose

Arabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde functional group.For biosynthetic reasons, most saccharides are almost always more abundant in nature as the "D"-form, or structurally analogous to D-glyceraldehyde.For sugars, the D/L...

 into D-xylulose-5-phosphate

Xylulose

Xylulose is a ketopentose, a monosaccharide containing five carbon atoms, and including a ketone functional group. It has the chemical formula 5105. In nature, it occurs in both the L- and D-enantiomers.- Pathology :...

, which is then metabolised via the pentose phosphate pathway

Pentose phosphate pathway

The pentose phosphate pathway is a process that generates NADPH and pentoses . There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars...

.
The initiator region, containing an operator site as well as a promoter, is called araI (the last letter of araI is an uppercase letter "i").
Near this site lies the araC gene, which encodes an activator protein.
The AraC protein binds to initiator region araI.

Metabolism of arabinose in E. coli

Substrate	Protein(s)	Function	Reversible	Product
L-arabinose Arabinose Arabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde functional group.For biosynthetic reasons, most saccharides are almost always more abundant in nature as the "D"-form, or structurally analogous to D-glyceraldehyde.For sugars, the D/L...	AraA	isomerase Isomerase In biochemistry, an isomerase is an enzyme that catalyzes the structural rearrangement of isomers. Isomerases thus catalyze reactions of the formwhere B is an isomer of A.-Nomenclature:...	yes	L-ribulose
L-ribulose Ribulose Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. It has chemical formula 5105. Two enantiomers are possible, D-ribulose and L-ribulose . D-Ribulose is the diastereomer of D-xylulose.Ribulose sugars are composed in the...	AraB	ribulokinase Ribulokinase In enzymology, a ribulokinase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are ATP, L-ribulose, and D-ribulose, whereas its 3 products are ADP, L-ribulose 5-phosphate, and D-ribulose 5-phosphate....	no	L-ribulose-phosphate
L-ribulose-phosphate	AraD	epimerase	yes	D-xylulose-phosphate

Activation

If arabinose is present, it builds a complex: AraC + arabinose

This complex is needed for RNA polymerase to bind to the promoter and transcribe the ara operon.
Also for activation the binding of another structure to araI is needed: CAP + cyclic AMP

So the activation depends on the presence of arabinose and cAMP.

Repression

If arabinose is absent, the AraC protein assumes a different conformation. In this conformation
the AraC protein binds to the araI DNA region as well as to the ara0 DNA region. This causes the DNA to form a loop, preventing transcription of the downstream ara operon elements.

Sequence of the Operon:

araC : araO : araI : araB : araA : araD

See also

• The lac operon
  Lac operon
  The lac operon is an operon required for the transport and metabolism of lactose in Escherichia coli and some other enteric bacteria. It consists of three adjacent structural genes, lacZ, lacY and lacA. The lac operon is regulated by several factors including the availability of glucose and of...
  
  is another operon in E. coli that has been a focus for research in gene expression.