L-arabinose operon
The L-arabinose operon, also called the ara or araBAD operon, is an operon that encodes enzymes needed for the catabolism of arabinose in Escherichia coli. It has both positive and negative regulation and is activated allosterically.[1]
It has been a focus for research in molecular biology since 1970, and has been investigated extensively at its genetic, biochemical, physiological, and biophysical levels.
In E. coli, arabinose is converted to xylulose 5-phosphate, an intermediate of the pentose phosphate pathway.[2]
Structure
The structural genes, which encode enzymes for arabinose catabolism, are araB, araA, and araD (collectively known as araBAD). The regulator gene is araC. The genes araBAD and araC are transcribed in opposite directions. [2]
- araA encodes L-arabinose isomerase, which catalyzes isomerization between L-arabinose and L-ribulose.
- araB encodes ribulokinase, which catalyzes phosphorylation of (L/D)-ribulose to form (L/D)-ribulose 5-phosphate.
- araD encodes L-ribulose-5-phosphate 4-epimerase, which catalyzes epimerization between L-ribulose 5-phosphate and D-xylulose 5-phosphate.
D-xylulose 5-phosphate and D-ribulose-5-phosphate are metabolites in the pentose phosphate pathway.
The operators are araI and araO2. The operators lie between the AraC.
AraI lies between the structural genes and the operator. The araI1 and araI2 are DNA-binding sites that, when occupied by AraC, induce expression.
| 5' | araC | araO | araI | araB | araA | araD | 3' |
|---|---|---|---|---|---|---|---|
| Regulator | Operator | Structural | |||||
(Distances not to scale)
Function
Repression
The ara operon is regulated by the AraC protein. If arabinose is absent, the dimer AraC protein represses the structural gene by binding to araI1 and araO2 and the DNA forms a loop. The loop prevents RNA polymerase from binding to the promoter of the ara operon, thereby blocking transcription.
Activation
When arabinose is present, arabinose binds AraC and prevents AraC from interacting. This breaks the DNA loop. The two AraC-arabinose complexes bind to the araI1 and araI2 sites which promotes transcription. When arabinose is present, AraC acts as an activator.
| Substrate | Protein(s) | Function | Reversible | Product |
|---|---|---|---|---|
| L-arabinose | AraA | isomerase | yes | L-ribulose |
| L-ribulose | AraB | ribulokinase | no | L-ribulose-phosphate |
| L-ribulose-phosphate | AraD | epimerase | yes | D-xylulose-phosphate |
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: CRP (formerly known as CAP) + cyclic AMP
So the activation depends on the presence of arabinose and cAMP.
See also
- The lac operon is another operon in E. coli that has been a focus for research in gene expression.
References
- ↑ Watson, James (2003). Molecular Biology of the Gene. p. 503.
- 1 2 Schleif, R. (2010). "AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action". FEMS Microbiology Reviews: no. doi:10.1111/j.1574-6976.2010.00226.x.