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Overview: Gene regulation in bacteria

Overview of operons, regulatory DNA sequences, & regulatory genes. Repressor & activator proteins.

Key points:

  • Bacterial genes are often found in operons. Genes in an operon are transcribed as a group and have a single promoter.
  • Each operon contains regulatory DNA sequences, which act as binding sites for regulatory proteins that promote or inhibit transcription.
  • Regulatory proteins often bind to small molecules, which can make the protein active or inactive by changing its ability to bind DNA.
  • Some operons are inducible, meaning that they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule.


We tend to think of bacteria as simple. But even the simplest bacterium has a complex task when it comes to gene regulation! The bacteria in your gut or between your teeth have genomes that contain thousands of different genes. Most of these genes encode proteins, each with its own role in a process such as fuel metabolism, maintenance of cell structure, and defense against viruses.
Some of these proteins are needed routinely, while others are needed only under certain circumstances. Thus, cells don't express all the genes in their genome all the time. You can think of the genome as being like a cookbook with many different recipes in it. The cell will only use the recipes (express the genes) that fit its current needs.

How is gene expression regulated?

There are various forms of gene regulation, that is, mechanisms for controlling which genes get expressed and at what levels. However, a lot of gene regulation occurs at the level of transcription.
Bacteria have specific regulatory molecules that control whether a particular gene will be transcribed into mRNA. Often, these molecules act by binding to DNA near the gene and helping or blocking the transcription enzyme, RNA polymerase. Let's take a closer look at how genes are regulated in bacteria.

In bacteria, genes are often found in operons

In bacteria, related genes are often found in a cluster on the chromosome, where they are transcribed from one promoter (RNA polymerase binding site) as a single unit. Such a cluster of genes under control of a single promoter is known as an operon. Operons are common in bacteria, but they are rare in eukaryotes such as humans.
In general, an operon will contain genes that function in the same process. For instance, a well-studied operon called the lac operon contains genes that encode proteins involved in uptake and metabolism of a particular sugar, lactose. Operons allow the cell to efficiently express sets of genes whose products are needed at the same time.

Anatomy of an operon

Operons aren't just made up of the coding sequences of genes. Instead, they also contain regulatory DNA sequences that control transcription of the operon. Typically, these sequences are binding sites for regulatory proteins, which control how much the operon is transcribed. The promoter, or site where RNA polymerase binds, is one example of a regulatory DNA sequence.
Most operons have other regulatory DNA sequences in addition to the promoter. These sequences are binding sites for regulatory proteins that turn expression of the operon "up" or "down."
  • Some regulatory proteins are repressors that bind to pieces of DNA called operators. When bound to its operator, a repressor reduces transcription (e.g., by blocking RNA polymerase from moving forward on the DNA).
  • Some regulatory proteins are activators. When an activator is bound to its DNA binding site, it increases transcription of the operon (e.g., by helping RNA polymerase bind to the promoter).
Where do the regulatory proteins come from? Like any other protein produced in an organism, they are encoded by genes in the bacterium's genome. The genes that encode regulatory proteins are sometimes called regulatory genes.
Many regulatory proteins can themselves be turned "on" or "off" by specific small molecules. The small molecule binds to the protein, changing its shape and altering its ability to bind DNA. For instance, an activator may only become active (able to bind DNA) when it's attached to a certain small molecule.

Operons may be inducible or repressible

Some operons are usually "off," but can be turned "on" by a small molecule. The molecule is called an inducer, and the operon is said to be inducible.
  • For example, the lac operon is an inducible operon that encodes enzymes for metabolism of the sugar lactose. It turns on only when the sugar lactose is present (and other, preferred sugars are absent). The inducer in this case is allolactose, a modified form of lactose.
Other operons are usually "on," but can be turned "off" by a small molecule. The molecule is called a corepressor, and the operon is said to be repressible.
  • For example, the trp operon is a repressible operon that encodes enzymes for synthesis of the amino acid tryptophan. This operon is expressed by default, but can be repressed when high levels of the amino acid tryptophan are present. The corepressor in this case is tryptophan.
These examples illustrate an important point: that gene regulation allows bacteria to respond to changes in their environment by altering gene expression (and thus, changing the set of proteins present in the cell).

Some genes and operons are expressed all the time

Many genes play specialized roles and are expressed only under certain conditions, as described above. However, there are also genes whose products are constantly needed by the cell to maintain essential functions. These housekeeping genes are constantly expressed under normal growth conditions ("constitutively active"). Housekeeping genes have promoters and other regulatory DNA sequences that ensure constant expression.

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