initially, how efficiently it supports isomer izat ion, and how readily the polymerase tan then escape. The correlation between promoter strength and sequence explains why promoters are so heterogeneous: some genes need to be expressed mote highly than others and the former are likely tn have sequences closer to the consensus.
An additional DNA element that binds RNA polymerase is found in some strong promoters, for example those directing expression of the ribosomal RNA (rRNA) genes. This is called an UP-eiement (see Figure 12-5b) and increases polymerase binding by providing an additional specific interaction between the enzyme and the DNA.
Another class of o7n-promoters lacks a —35 region and instead has a so-called "extended —10" element. This comprises a standard —10 re-ginn with an additional short sequence element at its upstream end. Extra contacts made between polymerase and this additional sequence element compensate for the absence of a -35 region. As we will see in Chapter IE, the gal genes of E. coli use such a promoter.
The cr Factor Mediates Binding of Polymerase to the Promoter
The rr70 factor can be divided into four regions called cr region t through o region 4 (see Figure 12-6), The regions that recognize the -10 and -35 elements of the promoter are region 2 and 4, respectively.
Two helices within region 4 form a common DNA-binding motif called a helix-turn-helix. One of these helices inserts into the major groove and interacts with bases in the —35 region; (he other lies across the top of the groove, making contacts with the DNA backbone. This structural motif is found in many DNA-binding proteins—for example, almost all transcriptional activators and repressors found in bacterial cells (described in Chapter 16)—and was discussed in detail in Chapter 5 (Figure 5-20).
The -10 region is also recognized by an a helix. But in this case, the interaction is less well-characterized and is more complicated for the following reason; whereas the —35 region simply provides binding energy to secure polymerase to the promoter, the —10 region has a more elaborate role in transcription initiation, because it is within that element that DNA melting is initiated in the transition from the
The DNA sequences of binding sites recognized by a given protein may not always be exactly the same. Likewise, a stretch of amino acids that bestows upon a protein a particular function may be slightly different in different proteins. A consensus sequence is, in each case, a version of the sequence having at each position the nucleotide (or amino acid) most commonly found there in different examples. Thus the consensus sequence for promoters in E coll recognized by RNA polymerase containing o7r- is shown in the figure (Box 12-1 Figure f). This consensus sequence was derived by aligning 500 sequences known to function as cr7n promoters and ascertaining the most common base found at each position in the -35 and in the 10 hexamers. That nucleotide is then chosen as the nucleotide of choice at that position in the consensus; its relative frequency and the frequencies with which the other three nucleotides occur at each position is portrayed in the graph. Note that there is no significant consensus among the 17 to 19 nucleotides that lie in the region between -35 and -10
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