Nature of the Signal Molecule

The substrate specificity and the inducer specificity of an operon need not be identical. One is determined by which molecules fit the active site(s) of the enzyme(s) of the pathway and the other by which molecules fit the binding site on the regulatory protein. In the case of the lactose operon allo-lactose, glyceryl-galactoside and IPTG are true inducers (i.e. they bind to the LacI protein). Lactose itself is only an apparent inducer, as it does not bind directly to LacI and must first be converted to allo-

araBAD operon Operon that encodes proteins involved in metabolism of the sugar arabinose arabinose A five-carbon sugar often found in plant cell wall material that can be used as a carbon source by many bacteria a//o-lactose An isomer of lactose that is the true inducer of the lac operon autogenous regulation Self regulation, i.e. when a DNA-binding protein regulates the expression of its own gene

FadR—An Example of a Repressor and an Activator

An example of differential binding of a DNA-binding protein is the FadR protein of E. coli. FadR represses the genes for fatty acid breakdown, but also activates certain genes involved in fatty acid synthesis. FadR responds to the availability of long-chain fatty acids in the growth medium. The cell can incorporate pre-made fatty acids into its lipids and can also break them down for energy. Fatty acids are taken up as coenzyme A derivatives, not free fatty acids; hence the signal mole cule recognized by FadR is a long-chain acyl-CoA. In the absence of acyl-CoA, FadR represses the operons for fatty acid degradation and also activates fabA, a gene involved in fatty acid biosynthesis. When the FadR protein binds acyl-CoA, it no longer binds to DNA. Fatty acid degradation is induced and in addition the level of expression of fabA decreases, so fewer fatty acids are manufactured.

Current Opinion in Structural Biology

FIGURE 9.15 FadR Structure and Binding

Overlay of FadR bound to DNA (in blue) and to myristoyl-CoA (in green). Atoms of myristoyl-CoA are shown as spheres. The HTH motif is colored red in the DNA-bound structures. From Huffman & Brennan, Current Opinion in Structural Biology 12 (2002) 98-106.

The same regulatory protein can sometimes turn genes on or off depending on where it binds on the DNA.

lactose. However, lactose, a/lo-lactose, and glyceryl-galactoside are all substrates of b-galactosidase whereas IPTG is not (Fig. 9.13, above).

For induction of the lac operon by lactose, low levels of both LacY (transport protein) and LacZ (b-galactosidase) proteins are necessary. The inducer must be transported into the cell before it can bind to LacI and b-galactosidase must convert some of the lactose to a/lo-lactose. In practice, when a gene is "switched off," it is not utterly inactive. Even when the lac operon is not induced, occasional mRNA molecules are made and a few molecules of LacY and LacZ are present. The maltose system allows transport and metabolism of maltose and longer oligosaccharides also made of glucose

FIGURE 9.16 AraC Repressor and Activator

A) AraC dimers are either activators or repressors depending on whether arabinose is bound or not. B) When AraC binds arabinose, the dimer changes configuration and binds to DNA at sites 1 and 2. Here it acts as an activator, allowing the RNA polymerase to bind. C) When the repressor form of AraC binds DNA, it occupies sites 2 and 3, forming a loop in the DNA and causing gene inactivation.

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