The Arabinose Operon

Written by Chinyere

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Arabinose is a five carbon sugar that can be used by E.coli as an alternative carbon source. The enzymes necessary for the metabolism of arabinose are coded for by the arabinose operon. The arabinose operon has a complex regulatory system. It was studied and explained by a scientist, Ellis Englesberg soon after the Jacob and Monod described the lac operon. He came to the conclusion that the arabinose operon can be regulated both positively and negatively in a similar manner as the lactose operon. Therefore the arabinose operon is also an inducible operon. In E.coli cells growing in the absence of arabinose, the three different enzymes involved in its metabolism are present in the cell in very small amounts and there is no expression of the operon. This is an adaptive mechanism that ensures that these enzymes needed to catabolize arabinose are only produced in sufficient amounts when arabinose is present in the environment. The arabinose operon also exhibits catabolite repression. A cAMP-CRP complex must be formed in order for the positive expression of the arabinose operon to occur. High levels of glucose in the environment will repress the arabinose operon due to low levels of the cAMP molecule. This is similar to the conditions necessary for lactose to be utilized as a carbon source. The arabinose operon will only express its genes if arabinose is the best carbon source present in the environment.

Structure and Mechanism

The arabinose operon consists of three structural genes, B, A and D that code for the catabolic enzymes: kinase, isomerase and epimerase respectively and a C gene, a conventional gene that produces a protein product that combines with arabinose and acts positively to “turn on” the arabinose operon. There are also two promoter sites, Pc and Pbad, two operator sites, O1 and O2 and an inducer site ara I, present in the arabinose operon.

High level functioning of the ara operon demands the simultaneous presence of two positive control indicators, the presence of arabinose as the best carbon source and a functional C gene. The ara C gene is an intriguing gene which controls the ara operon both positively and negatively. It encodes a regulatory protein. It has three binding sites, O1, O2 and ara I. In the absence of arabinose the regulatory protein binds simultaneously to the ara I and O2 regions causing the operon to fold on itself thereby blocking transcription of the ara B, A and D genes. However, when arabinose is present, it binds to the ara C gene product and stimulates the transcription of the structural B, A and D genes. The cAMP-CRP complex acts by promoting a rearrangement of the ara C gene when arabinose is present. In rearrangement, it represses transcription to a state in which it activates promoter, Pbad of the ara B, A and D genes.

The ara C gene also regulates the expression of its own gene product. Thus, it is an autoregulator. Only when the levels of its gene product become low, does the ara C gene activate its promoter, Pc and code for its gene product regardless of the levels of arabinose present in the environment.

The structural genes B, A and D code for enzymes for the catabolysis of arabinose. The ara A gene codes for isomerase which breaks down arabinose to L-ribulose. The ara B gene encodes for its enzyme, kinase which breaks down L-ribulose to L-ribulose-5-phosphate, which if it accumulates, becomes toxic to the cell. This can only occur if there is a mutation in the ara D gene preventing the further break down of the substrate. The ara D gene then codes for its gene product, epimerase which breaks down L-ribulose-5-phosphate to D-xyulose-5-phosphate and this compound is further broken down through a glycolytic pathway.

Mutations In The Arabinose Operon

There are several mutations that could prevent the expression of the arabinose operon genes and even cause the cell to die. A mutation in the ara A gene will cause the bacterial cell to become arabinose negative. This means that the bacterium can no longer use arabinose as a carbon source. It will not utilize it if the cell is grown in a minimal media containing arabinose,. A mutation in the ara B gene will also result in the same state. However, a mutation in the ara D gene will result in cell death. After the ara B gene product degrades L-ribulose to L-ribulose-5-phosphate, epimerase is not synthesized and cannot break down L-ribulose-5-phosphate which accumulates in the cell. L-ribulose-5-phosphate is toxic to the cell when present in high levels.

Mutations could also occur in the ara C gene causing the promoters, Pbad and Pc, to become inactive and the arabinose operon remains permanently repressed.