In the previous article we saw how RNA polymerase determines how to start transcription. In this article, we will examine how they decide to end transcription.

Before we dive in, however let’s take some time to remind ourselves of the lay of the land. So far, we are well familiar with the happenings at the promotor. As you should recall, that is where RNA polymerase binds. Further upstream at the distal elements is where you might find binding proteins like pTrpR. The arrow immediately to the right of the proximal promotor is the transcriptional start site we refer to as “+1”. Further downstream where you see the second arrow is where you will find the start codon (AUG). This is where RNA polymerase begins to transcribe until it gets to a transcriptional termination signal (the second arrow in the green coding region). Two mechanisms are responsible for termination at this site. They are intrinsic (or rho independent termination) and extrinsic (or rho dependent termination).

Rho-dependent Termination

Intrinsic Termination

As the RNA is elongated during transcription, it has the ability to base-pair with itself to form a secondary structure called a “hairpin loop”. This hairpin loop is formed within the RNA polymerase complex due to GC-rich inverted repeat regions. Guanine-cytosine (GC) bonds are strong and stable since they have 3 hydrogen bonds compared to adenine-thymine (AT) interactions with only two hydrogen bonds.

Hairpin loops slow down the RNA polymerase but is generally not enough to cause it to stop transcribing. However, if the hairpin is followed by a series of uracil (usually 6 or more), it falls off the DNA and transcription stops. The separation is associated with the weak interaction that uracil forms with the DNA template.

Attenuation – The trp Operon

In the previous lesson you learned that the Trp operon is controlled by an operator that can be turned off or on depending on whether or not pTrpR is binding to the DNA. However, there is more to the story. Consider the diagram below showing the Trp operon with an open stretch of DNA. After the operator (O) there is a region that is labelled as 1, 2, 3, and 4. These regions have the capability of base pairing on each other.

  1. Region 1 can base pair with region 2
  2. Region 2 can base pair with region 3
  3. Region 3 can base pair with region 4

Region 4 is followed by a run of U’s. Whenever regions 3 and 4 binds, transcription is terminated (an intrinsic factor as you should recall).

The same regions are illustrated in the following diagram in more detail. Notice the run of uracil after region 4. You should also notice that region 1 contains the tryptophan codon at two places.

Trp operon Attenuation Regions

Why is this significant? For that, you need to look at the next diagram.

The diagram shows transcription and translation of the TrpL gene, both taking place at the same time. This is not surprising since this is the versatility that prokaryotes have compared to eukaryotes.

As you can see, tryptophan levels are low. When this happens, the ribosomes are not able to find tryptophan to add to the growing chain. Hence it will pause. During this pause, region 1 of the DNA gets covered. Since region 1 is covered, it cannot base pair with region 2. Hence regions 2 and 3 will base pair instead. This base pairing will cause the RNA polymerase to stall but will not kick off the RNA polymerase. Instead, the RNA polymerase will continue downstream to express the genes needed for tryptophan production.

Now let’s see what happens when tryptophan levels are high. For that, check out the next diagram.

Notice that with abundant tryptophan the ribosomes will bring in the needed tryptophan and incorporate them in the leader peptide. After that the ribosome arrives at a translational stop codon where they pause and in the process, cover regions 1 and 2. In the meantime, regions 3 and 4 forms a base pair. Remember that region 4 carries a string of uracil that triggers termination. Therefore, when tryptophan levels are high, RNA polymerase is kicked off the DNA preventing transcription of the genes required to make tryptophan.

Extrinsic Termination

Extrinsic termination utilizes a protein called rho. Rho is a hexamer which binds to the rho-binding site and burns ATP to move 5′ to 3′ at a rate of 200 nucleotides per second (at least twice as fast as RNA polymerase) unless blocked by translating ribosomes. When it bumps into the RNA polymerase, RNA polymerase gets the signal to stop transcription.

The application of the rho factor can be observed in the lac operon. If the lacZ is defective, it causes the ribosome to stall in translation allowing the RNA polymerase to pull well ahead of the ribosome. This widens the gap between them and leaves a “naked” region on the DNA upon which rho can bind. Once rho binds to the RNA, it races towards the RNA polymerase, bumps into it, and causes it to fall off the DNA, terminating transcription. This is a brilliant move since any defect in the DNA that prevents the formation of one of the proteins would make it of no use to make the others. All must be present together.

Reference: Krane, D. 2021. Bio 2110 Molecular Biology Video Lecture. Wright State University – Lake Campus.

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Courtney Simons
Courtney Simons
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Courtney Simons is a food science professor. He holds a BS degree in food science and a Ph.D. in cereal science from North Dakota State University.