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The L-arabinose operon, also called the ara or araBAD operon, is an operon required for the breakdown of the five-carbon sugar, L-arabinose, in Escherichia coli. L-arabinose operon contains three structural genes: araB, araA, araD (collectively known as araBAD), which encode for three metabolic enzymes that are required for the metabolism of L-arabinose. AraB (Ribulokinase), AraA (Isomerase), AraD (Epimerase) produced by these genes catalyze conversion of L-arabinose to an intermediate of pentose phosphate pathway, D-xylulose-5-phosphate.

The structural genes of the L-arabinose operon are transcribed from a common promoter into a single transcript i.e. mRNA. The expression of L-arabinose operon is controlled as a single unit by the product of regulatory gene araC and the catabolite activator protein (CAP)-cAMP complex. The regulator protein AraC is sensitive to the level of arabinose and plays a dual role as both an activator in the presence of arabinose and a repressor in the absence of arabinose to regulates the expression of araBAD. AraC protein not only controls the expression of araBAD, but also auto-regulates its own expression at high AraC levels.

Structure
L-arabinose operon is composed of structural genes and regulatory regions including the operator region (araO1, araO2) and the initiator region (araI1, araI2). The structural genes, araB, araA and araD, encode enzymes for L-arabinose catabolism. There is also a CAP binding site where CAP-cAMP binds to and facilitates catabolite repression. i.e. positive regulation of araBAD.

The regulatory gene,araC, is located upstream of L-arabinose operon and is encoded for arabinose-responsive regulatory protein AraC. Both araC and araBAD have a discrete promoter where RNA polymerase bound and initiate transcription. In which, araBAD and araC are transcribed in opposite direction from the araBAD promoter (PBAD) and araC promoter (PC) respectively.

Function

 * araA encodes for L-arabinose isomerase, which catalyzes isomerization between L-arabinose and L-ribulose.
 * araB encodes for ribulokinase, which catalyzes phosphorylation of L-ribulose to form L-ribulose-5-phosphate.
 * araD encodes for L-ribulose-5-phosphate 4-epimerase, which catalyzes epimerization between L-ribulose 5-phosphate and D-xylulose-5-phosphate.

In which, both L-ribulose 5-phosphate and D-xylulose-5-phosphate are involved in the pentose phosphate pathway and produce reducing power.

Regulation
The L-arabinose system is not only under the control of CAP-cAMP activator, but also positively or negatively regulated through binding of AraC protein. AraC functions as a homodimer which can control transcription of araBAD through interaction with the operator and the initiator region on L-arabinose operon. Each AraC monomer composed of two domains including a DNA binding domain and a dimerization domain. The dimerization domain is responsible for arabinose-binding. AraC undergoes conformational change upon arabinose-binding, in which, it has two distinct conformations. The conformation is purely determined by the binding of allosteric inducer arabinose.

AraC can also negatively autoregulates its own expression when the concentration of AraC becomes too high. AraC synthesis is repressed through binding of dimeric AraC to the operator region (araO1).

Negative regulation of araBAD
When arabinose is absent, cells do not need PBAD product for breaking down arabinose. Therefore, dimeric AraC acts as a suppressor by which one monomer binds to the operator of the araBAD gene (araO2), another monomer binds to a distant DNA half site known as araI1. This leads to the formation of a DNA loop. This orientation blocks RNA polymerase from binding to the araBAD promoter. Therefore, transcription of structural gene araBAD is inhibited.

Positive regulation of araBAD
Expression of the araBAD operon is activated in the absence of glucose and in the presence of arabinose. When arabinose is present, both AraC and CAP work together and function as activators.

Via AraC
AraC acts as an activator in the presence of arabinose. AraC undergoes a conformational change when arabinose bind to the dimerization domain of AraC. As a result, AraC-arabinose complex falls off from araO2 and breaks the DNA loop. Hence, it is more energetically favorable for AraC-arabinose to bind to two adjacent DNA half sites: araI1 and araI2 in the presence of arabinose. In which, one of the monomers binds araI1, the remaining monomer binds araI2. In other words, Binding of AraC to araI2 is allosterically induced by arabinose. One of the AraC monomers places near to the araBAD promoter in this configuration, which helps to recruit RNA polymerase to the promoter to initiate transcription.

Via CAP/cAMP (Catabolite Repression)
CAP act as a transcriptional activator only in the absence of preferred sugar, glucose. When glucose is absent, high level of CAP protein/cAMP complex bind to CAP binding site, a site between araI1 and araO1. Binding of CAP/cAMP is responsible for opening up the DNA loop between araI1 and araO2, also increase the binding affinity of AraC protein for araI2. Thereby, promoting RNA polymerase to bind to araBAD promoter and switches on expression of araBAD required for metabolising L-arabinose.



Autoregulation of AraC
The expression of araC is negatively regulated by its own protein product, AraC. The excess AraC binds to the operator of the araC gene, araO1, at high AraC levels, which physically blocks the RNA polymerase from accessing the araC promoter. Therefore, prevents the transcription of araC from araC promoter. i.e. AraC protein inhibits its own expression at high concentrations.

Use in protein expression system
L-arabinose operon has been a focus for research in molecular biology since 1970, and has been investigated extensively at its genetic, biochemical, physiological and biotechnical levels. The L-arabinose operon has been commonly used in protein expression system, as the araBAD promoter can be used for producing an excessive level of targeted expression under tight regulation. By fusing araBAD promoter to a gene of interest, the expression of the target gene can be solely regulated by arabinose. i.e. constitutive expression of the gene of interest is permitted as long as arabinose is present.