A typical gene is sw itched on and ofF in response to the need for its product. This regulation is predominantly at the level of transcription initiation. Thus, for example, in E. coli, a gene encoding the enzyme that metabolizes lactose is tran scribed at high levels only when lactose is available in the growth medium. Furthermore, when glucose (a better energy source) is also available, the gene is not expressed even when lactose is present.

Signals, such as the presence of a specific sugar, are communicated to genes by regulatory proteins. These are of two types: pctivafore, positive regulators that switch genes on; and repressors, negative regulators that switch genet; nil. Typically these regulators are DNA-binding proteins thai recognize specific sites at or near the genes they control

Activators, in the simplest (and most common) cases, work, on promoters that are inherently weak. That is, RNA polymerase .binds to the promoter (and thus initiates transcription) poorly in the absence of any regulator. An activator binds to DNA with one surface and with another surface binds polymerase and recruits it to the promoter. This process is an example of cooperative binding, and is sufficient to stimulate transcription.

Repressors can inhibit transcription by binding to a site that overlaps the promoter, thereby blocking KNA polymerase binding. Repressors can work in other ways as well, for example by binding to a site beside the promoter and. by interacting with polymerase bound at the promoter, inhibiting initiation.

The lac: genes of E. roli are controlled hy an activator and a repressor that work in the simplest way ¡est outlined CAP in the absence of glucose, binds DNA near the lac promoter and, by recruiting polymerase to that promoter, activates expression of those genes. The Lac repressor binds a site that overlaps the promoter and stmts off expression in die absence of lactose.

Another way in which RNA polymerase is recruited to different genes is by the use of alternative a factors. Thus, different o factors can replace the most prevalent one (rr" in E. roli) and direct the enzyme to promoters of different sequences. Examples include <t)2, which directs transcription of genes in response to heat shock, and ir'\ which directs transcription of genes involved in nitrogen metabolism Phage SPO] uses a series of alternative a to control the ordered expression of its genes during infection

There am. in bacteria, examples of other kinds of transcriptional activation as well. Thus, at some promoters, RNA jMjlymerase hinds efficiently unaided, and forms a stable, but inactive, closed complex. That closed complex does not spontaneously undergo transition to die open complex and initiate transcription. At such a promoter, an activator must stimulate the transition from closed to open complex.

Activators that stimulate this kind of promoter work by allostery: they interact with the stable closed complex and induce a ronformational change that causes transition to the open complex, in this chapter we saw two examples of transcriptional activators working by allostery. in one case, the activator (NtrC) interacts with the RNA polymerase (bearing trM) bound in a stable closed complex at the glnA promoter, stimulating transition to the open complex, in the other example, the activator (MerR) induces a conformational change in the merT promoter DNA.

In all the cases we have considered, the regulators themselves are coril rolled allosterically by signals. That is, the shape of the regulator changes in the presence of its signal: in one state it can bind DNA, in the other it cannot. Thus, for example, the Lac repressor is cor limited by the ligand allolactose (a product made from lactose). When allolactose binds repressor it induces a change in the shape of that protein; in that state the protein cannot bind DNA.

Gene expression can be regulated at steps after transcription initiation. For example, regulation can be at the level of transcriptional elongation. Three cases were discussed here: attenuation at tin1 tip genes and antiterniina-tion by the N and Q proteins of phage X. The trp genes encode enzymes required for the synthesis of the amino acid tryptophan. These genes are only transcribed when the cell lacks tryptophan. One way that amino acid con trols expression of these genes is attenuation: a transcript initiated at the trp promoter aborts before it transcribes the structural genes if there is tryptophan [in the form of Trp tKNAs) available in the cell. The X proteins N and Q load 011 to RNA polymerases initiating transcription at certain promoters in the phage genome. Once modified in this way, the enzyme can pass through certain transcriptional terminator sites that would otherwise block expression of downstream genes. Beyond transcription, we saw an example of gene regulation that operated at the level of translation of mRNA {the case we described was that of the tibosomal protein genes).

We concluded this chapter with a detailed discussion of how bacteriophage X chooses between two alternative modes of propagation. Several of the strategies of gene regulation encountered in this system turn out to operate in other systems as well, including, as we will see in later chapters, those that govern the development of animals— for example, the use of cooperative binding to give stringent on/off switches; and the use of separate pathways for establishing and maintaining expression of genes.

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