Arabinose Operon is a self-regulatory sequence of genes used by material to metabolize a five-carbon sugar called arabinose when there is a deficiency of glucose in the environment.

1. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
ARABINOSE OPERON
“The Arabinose operon (alternative names: L-arabinose operon, ara operon, and araBAD
operon) is an operon required for the breakdown of the five-carbon sugar, L-arabinose, in
Escherichia coli.”
“An operon is a functioning unit of DNA containing a cluster of genes under the control of a
single promoter. The genes are transcribed together into an mRNA strand (polycistronic) and
are translated together in the cytoplasm, i.e. arabinose operon.”
STRUCTURE OF ARABINOSE OPERON:
L-arabinose operon is composed of the following:
 Control sites include 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 the CAP-cAMP complex binds to and facilitates
catabolite repression, and results in positive regulation of araBAD when the cell is starved
of glucose (when there is a glucose deficiency).
 The regulatory gene, araC, is located upstream of the L-arabinose operon and encodes
the regulatory protein AraC.
 Both araC and araBAD have a discrete promoter where RNA polymerase binds and
initiates transcription. Promoter of araC is denoted as ParaC / P(araC), whereas the
promoter of araBAD is denoted as ParaBAD / P(araBAD).
Figure: Structure of arabinose operon. (Source: Wikimedia, CC-BY-SA)
FUNCTIONS OF araBAD GENES:
 araA encodes L-arabinose isomerase, which catalyzes isomerization between L-arabinose
and L-ribulose.

2. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
 araB encodes ribulokinase, which catalyzes phosphorylation of L-ribulose to form L-
ribulose-5-phosphate.
 araD encodes L-ribulose-5-phosphate 4-epimerase, which catalyzes epimerization
between L-ribulose 5-phosphate and D-xylulose-5-phosphate.
Figure: Function of araBAD genes. (Source: Wikimedia, CC-BY-SA)
Both L-ribulose 5-phosphate and D-xylulose-5-phosphate are metabolites of the pentose
phosphate pathway, i.e. they can be used by the cell.
REGULATION OF ARABINOSE OPERON:
Arabinose operon is regulated both negatively (repression) and positively. The regulation of
arabinose operon takes place as follows:
Negative regulation of araBAD: When arabinose is absent, cells do not need the araBAD
products for breaking down arabinose. Therefore, dimeric AraC (two units of AraC bound
together) acts as a repressor: 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.
Figure: Formation of DNA loop in ara operon, inhibiting translation. (Source: Wikimedia, CC-
BY-SA)
Positive regulation of araBAD: Expression of the araBAD operon is activated in the absence
of glucose and the presence of arabinose. When arabinose is present, both AraC and CAP
work together and function as activators.

3. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
Role of AraC: AraC acts as an activator in the presence of arabinose, i.e. it undergoes a
conformational change and breaks the DNA loop. It also helps in initiating transcription.
CAP-cAMP (catabolite repression): CAP acts as a transcriptional activator only in the absence
of E. coli's preferred sugar, glucose. When glucose is absent, a high level of CAP protein/cAMP
complex binds to the CAP binding site, situated between araI1 and araO1. Binding of
CAP/cAMP is responsible for opening up the DNA loop, thereby promoting RNA polymerase
to bind to araBAD promoter.
Autoregulation of AraC: The expression of araC is negatively regulated by its 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,
the AraC protein inhibits its expression at high concentrations.
EFFECT OF MUTATIONS ON ara GENES:
Point mutations in the genetic sequences of any on the ara genes can have far reaching
consequences for the bacterial metabolism:
 Mutations in ara-C gene (this gene controls the expression of the 3 structural genes) lead
to a super-repressed condition where ara-A, ara-B, and ara-D (3 structural genes) are shut
down even when arabinose is abundant, i.e. arabinose operon is shut down.
 A mutation in ara-A gene will cause the bacteria to become arabinose negative, i.e. it will
not be able to use arabinose as a carbon source.
 A mutation in ara-B gene will also make the bacteria arabinose negative.
 A mutation in ara-D gene will result in cell death due to the accumulation of ribulose 5-
phosphate which is toxic to the cell in high concentrations.