Introduction to The Prokaryotic Transcription

KEY CONCEPT
Transcription is 5′ to 3′ on a template that is 3′ to 5′.

Transcription produces an RNA chain identical in sequence with one strand of the DNA, sometimes called the coding strand. This strand is made 5′ → 3′ and is complementary to (i.e., it base pairs with) the template, which is 3′ → 5′. The RNA-like strand therefore is called the nontemplate strand, and the one that serves as the template for synthesis of the RNA is called the template strand, as shown in FIGURE 1.

FIGURE .1 The function of RNA polymerase is to copy one strand of duplex DNA into RNA.
RNA synthesis is catalyzed by the enzyme RNA polymerase. Transcription starts when RNA polymerase binds to a special region, called the promoter, at the start of the gene. The promoter includes the first base pair that is transcribed into RNA (the start point), as well as surrounding bases. From this position, RNA polymerase moves along the template, synthesizing RNA until it reaches a terminator sequence, where the transcript ends. Thus, a transcription unit extends from the promoter to the terminator.
The critical feature of the transcription unit, depicted in FIGURE .2, is that it constitutes a stretch of DNA used as a template for the production of a single RNA molecule. A transcription unit may encode more than one gene or cistron.

FIGURE 2. A transcription unit is a sequence of DNA transcribed into a single RNA, starting at the promoter and ending at the terminator.
Sequences prior to the start point are described as upstream of it; those after the start point (within the transcribed sequence) are downstream of it. Sequences are usually written so that transcription proceeds from left (upstream) to right (downstream).
This corresponds to writing the mRNA in the usual 5′ → 3′ direction. The DNA sequence often is written to show only the nontemplate strand, which (as mentioned earlier) has the same sequence as the RNA. Base positions are numbered in both directions away from the start point, which is called +1; numbers increase as they go downstream. The base before the start point is numbered −1, and the negative numbers increase going upstream. (No base is assigned the number 0.)
The initial transcription product, containing the original 5′ end, is called the primary transcript. rRNA and tRNA primary transcripts go through a maturation process in which sequences at the ends are cleaved off (“processed”) by endonucleases. The mature products from rRNA and tRNA operons are stable, approaching the generation time of the bacterium. In contrast, mRNA primary transcripts are subject to almost immediate attack by endonucleases and exonucleases. Thus, bacterial mRNA lifetimes
average only 1 to 3 minutes. In eukaryotes, rRNA and tRNA transcripts are processed, and the resulting products are stable, as in bacteria. However, eukaryote mRNA is much more stable than bacterial mRNA. 
Transcription is the first stage in gene expression and is the step at which it is regulated most often. Regulatory factors often determine whether a particular gene is transcribed by RNA polymerase, and subsequent stages in transcription and other steps in gene expression are also regulated frequently.
Two important questions in transcription are: How does RNA polymerase find promoters on DNA? This is a particular example of a more general question: How do proteins distinguish their specific binding sites in DNA from other sequences?
How do regulatory proteins interact with RNA polymerase (and with one another) to activate or to inhibit specific steps during initiation, elongation, or termination of transcription? In this chapter, we describe the interactions of bacterial RNA polymerase with DNA from its initial contact with the promoter, through the act of transcription, to its release from the DNA when the transcript has been completed.