Antitermination was discovered in bacteriophage infections. A common feature in the control of phage infection is that very few of the phage genes can be transcribed by the bacterial host RNA polymerase. Among these genes, however, are regulators whose products allow the next set of phage genes to be expressed. One of these types of regulator is an antitermination protein. In the absence of the antitermination protein, RNA polymerase terminates at the terminator. When the antitermination protein is present, it continues past the terminator.
The best characterized example of antitermination is provided by lambda phage, in which the phenomenon was discovered. It is used at two stages of phage expression. The antitermination protein produced at each stage is specific for the particular transcription units that are expressed at that stage.
The host RNA polymerase initially transcribes two genes, which are called the immediate early genes (N and cro). The transition to the next stage of expression is controlled by preventing termination at the ends of the immediate early genes, with the result that the delayed early genes are expressed. The antitermination protein pN acts specifically on the immediate early transcription units. Later during infection, another antitermination protein pQ acts specifically on the late transcription unit, to allow its transcription to continue past a termination sequence.
The different specificities on pN and pQ establish an important general principle: RNA polymerase interacts with transcription units in such a way that an ancillary factor can sponsor antitermination specifically for some transcripts. Termination can be controlled with the same sort of precision as initiation.
The antitermination activity of pN is highly specific, but the antitermination event is not determined by the terminators t and t; the recognition site needed for antitermination lies upstream in the transcription unit, that is, at a different place from the terminator site at which the action eventually is accomplished.
The recognition sites required for pN action are called nut (for N utilization). The sites responsible for determining leftward and rightward antitermination are described as nut and nut, respectively.
When pN recognizes the nut site, it forms a persistent antitermination complex in cooperation with a number of E. coli host proteins. These include three host Nus proteins, NusA, B, and C. NusA is an interesting protein. By itself in E. coli, it is part of the transcription termination system. However, when co-opted by N, it participates in antitermination. The complex must act on RNA polymerase to ensure that the enzyme can no longer respond to the terminator. The variable locations of the nut sites indicate that this event is linked neither to initiation nor to termination, but can occur to RNA polymerase as it elongates the RNA chain past the nut site. Phages that are related to lambda have different N genes and different antitermination specificities. The region on the phage genome in which the nut sites lie has a different sequence in each of these phages, and each phage must therefore have characteristic nut sites recognized specifically by its own pN. Each of these pN products must have the same general ability to interact with the transcription apparatus in an antitermination capacity, but each product also has a different specificity for the sequence of DNA that activates the mechanism.