For convenience, the nucleotide sequence of a single strand of DNA is shown; in reality, promoters are double-stranded by the σ factor. These common features are often summarized in the form of a consensus sequence (Figure 6–12). A consensus nucleotide sequence is derived by comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position. It therefore serves as a summary or “average” of a large number of individual nucleotide sequences. A more accurate way of displaying the range of DNA sequences recognized by a protein is through the use of a sequence logo, which reveals the relative frequencies of each nucleotide at each position (Figure 6–12C).
The DNA sequences of individual bacterial promoters differ in ways that determine their strength (the number of initiation events per unit time of the promoter). Evolutionary processes have fine-tuned each to initiate as often as necessary and have thereby created a wide spectrum of promoter strengths. Promoters for genes that code for abundant proteins are much stronger than those associated with genes that encode rare proteins, and the nucleotide sequences of their promoters are responsible for these differences.
Like bacterial promoters, transcription terminators also have a wide range of sequences, with the potential to form a simple hairpin RNA structure being the most important common feature. Since an almost unlimited number of nucleotide sequences have this potential, terminator sequences are even more heterogeneous than promoter sequences.
We have discussed bacterial promoters and terminators in some detail to illustrate an important point regarding the analysis of genome sequences. Although we know a great deal about bacterial promoters and terminators and can construct consensus sequences that summarize their most salient features, their variation in nucleotide sequence makes it difficult to definitively locate them simply
DNA. The nucleotides shown in the figure are recognized by σ factor, a subunit of  the RNA polymerase holoenzyme.
(B) The distribution of spacing between the –35 and –10 hexamers found in E. coli promoters. (C) A sequence logo displaying the same information as in panel (A). Here, the height of each letter is proportional to the frequency at which that base occurs at that position across a wide variety of promoter sequences. The total height of all the letters at each position is proportional to the information content (expressed in bits) at that position. For example, the total information content of a position that can tolerate several different bases is small (see the last three bases of the –35 sequences), but statistically greater than random.
DNA of E. coli chromosome gene a by analysis of the nucleotide sequence of a genome. It is even more difficult to locate analogous sequences in eukaryotic genomes, due in part to the excess DNA carried in these genomes. Often we need additional information, some of it from direct experimentation, to locate and accurately interpret the short DNA signals in genomes.
As shown in Figure 6–11, promoter sequences are asymmetric, ensuring that RNA polymerase can bind in only one orientation. Because the polymerase can synthesize RNA only in the 5ʹ-to-3ʹ direction, the promoter orientation specifies the strand to be used as a template. Genome sequences reveal that the DNA strand that is used as the template for RNA synthesis varies from gene to gene, depending on the orientation of the promoter (Figure 6–13).
Having considered transcription in bacteria, we now turn to the situation in eukaryotes, where the synthesis of RNA molecules is a much more elaborate affair.
In contrast to bacteria, which contain a single type of RNA polymerase, eukaryotic nuclei have three: RNA polymerase I, RNA polymerase II, and RNA polymerase
III. The three polymerases are structurally similar to one another and share some common subunits, but they transcribe different categories of genes (Table 6–2). RNA polymerases I and III transcribe the genes encoding transfer RNA, ribosomal RNA, and various small RNAs. RNA polymerase II transcribes most genes, including all those that encode proteins, and our subsequent discussion therefore focuses on this enzyme.