Transcription start site

Template strand

RNA transcript 5'

113.11 In bacterial promoters, consensus sequences are found upstream of the start site, approximately at positions -10 and -35.

Different genes are transcribed with different frequencies, and promoter binding is primarily responsible for determining the frequency of transcription for a particular gene. Promoters also have different affinities for RNA polymerase. Even within a single promoter, the affinity can vary over time, depending on its interaction with RNA poly-merase and a number of other factors.

Bacterial promoters Essential information for the transcription unit—where it will start transcribing, which strand is to be read, and in what direction the RNA poly-merase will move —is imbedded in the nucleotide sequence of the promoter. Promoters are sequences in the DNA that are recognized by the transcription apparatus and are required for transcription to take place. In bacterial cells, promoters are usually adjacent to an RNA coding sequence. The examination of many promoters in E. coli and other bacteria reveals a general feature: although most of the nucleotides within the promoters vary in sequence, short stretches of nucleotides are common to many. Furthermore, the spacing and location of these nucleotides relative to the transcription start site are similar in most promoters. These short stretches of common nucleotides are called consensus sequences.

The term "consensus sequence" refers to sequences that possess considerable similarity or consensus. By definition, the consensus sequence comprises the most commonly encountered nucleotides found at a specific location. For example, consider the following nucleotides found near the transcription start site of four prokaryotic genes.

5' -TAAAAT-3' Consensus sequence = 5' - T A T A A T - 3'

If two bases are equally frequent, they are designated by listing both bases separated by a line or a slash, as in 5 ' -T A T A A A/T- 3'. Purines can be indicated by the abbreviation R, pyrimidines by Y, and any nucleotide by N. For example, the consensus sequence 5 ' -T A Y A R N A- 3'

means that the third nucleotide in the consensus sequence (Y) is usually a pyrimidine, but either pyrimidine is equally likely. Similarly, the fifth nucleotide in the sequence (R) is most likely one of the purines, but both are equally frequent. In the sixth position (N), no particular base is more common than any other. The presence of consensus in a set of nucleotides usually implies that the sequence is associated with an important function. Consensus exists in a sequence because natural selection has favored a restricted set of nucleotides in that position.

The most commonly encountered consensus sequence, found in almost all bacterial promoters, is located just upstream of the start site, centered on position —10. Called the —10 consensus sequence or, sometimes, the Pribnow box, its sequence is

often written simply as TATAAT (< Figure 13.11). Remember that TATAAT is just the consensus sequence— representing the most commonly encountered nucleotides at each of these positions. In most prokaryotic promoters, the actual sequence is not TATAAT (< Figure 13.12).

Another consensus sequence common to most bacterial promoters is TTGACA, which lies approximately 35 nucleotides upstream of the start site and is termed the —35 consensus sequence (see Figure 13.11). The nucleotides on either side of the — 10 and —35 consensus sequences and those between them vary greatly from promoter to promoter, suggesting that they are relatively unimportant in promoter recognition.

The function of these consensus sequences in bacterial promoters has been studied by inducing mutations at various positions within the consensus sequences and observing the effect of the changes on transcription. The results of these studies reveal that most base substitutions within the — 10 and — 35 consensus sequences reduce the rate of transcription; these substitutions are termed down mutations because they slow down the rate of transcription. Occasionally, a particular change in a consensus sequence increases the rate of transcription; such a change is called an up mutation.

16-18 base pairs

6-7 base pairs

Promoter trp tRNATyr

-35 region

6-7 base pairs

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